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#
#
#
data_cif_img.dic
_datablock.id cif_img.dic
_datablock.description
;
##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.7.10 #
# of 2014-04-25 #
# ################################################################### #
# # *** 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. #
##############################################################################
##############################################################################
# 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
# _array_data.variant
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
# _array_element_size.variant
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.details
# _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
# _array_intensities.variant
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.compression_type_flag
# _array_structure.encoding_type
# _array_structure.id
# _array_structure.variant
#
# 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
# _array_structure_list.variant
#
# category ARRAY_STRUCTURE_LIST_SECTION
#
# _array_structure_list_section.array_id
# _array_structure_list_section.id
# _array_structure_list_section.index
# _array_structure_list_section.end
# _array_structure_list_section.start
# _array_structure_list_section.stride
# _array_structure_list_section.variant
#
# 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
# _array_structure_list_axis.variant
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.equipment_component
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.rotation
# _axis.rotation_axis
# _axis.type
# _axis.system
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
# _axis.variant
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.array_section_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
# _diffrn_data_frame.variant
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.gain_setting
# _diffrn_detector.id
# _diffrn_detector.layer_thickness
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
# _diffrn_detector.variant
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
# _diffrn_detector_axis.variant
#
# 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
# _diffrn_detector_element.variant
#
# 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
# _diffrn_measurement.variant
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
# _diffrn_measurement_axis.variant
#
# 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.polarizn_Stokes_I
# _diffrn_radiation.polarizn_Stokes_Q
# _diffrn_radiation.polarizn_Stokes_U
# _diffrn_radiation.polarizn_Stokes_V
# _diffrn_radiation.polarisn_norm_esd
# _diffrn_radiation.polarisn_ratio_esd
# _diffrn_radiation.polarizn_source_norm_esd
# _diffrn_radiation.polarizn_source_ratio_esd
# _diffrn_radiation.polarizn_Stokes_I_esd
# _diffrn_radiation.polarizn_Stokes_Q_esd
# _diffrn_radiation.polarizn_Stokes_U_esd
# _diffrn_radiation.polarizn_Stokes_V_esd
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
# _diffrn_radiation.variant
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
# _diffrn_refln.variant
#
# 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
# _diffrn_scan.time_period
# _diffrn_scan.time_rstrt_incr
# _diffrn_scan.variant
#
# 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
# _diffrn_scan_axis.variant
#
# 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.polarizn_Stokes_I
# _diffrn_scan_frame.polarizn_Stokes_Q
# _diffrn_scan_frame.polarizn_Stokes_U
# _diffrn_scan_frame.polarizn_Stokes_V
# _diffrn_scan_frame.polarizn_Stokes_I_esd
# _diffrn_scan_frame.polarizn_Stokes_Q_esd
# _diffrn_scan_frame.polarizn_Stokes_U_esd
# _diffrn_scan_frame.polarizn_Stokes_V_esd
# _diffrn_scan_frame.scan_id
# _diffrn_scan_frame.time_period
# _diffrn_scan_frame.time_rstrt_incr
# _diffrn_scan_frame.variant
#
# 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
# _diffrn_scan_frame_axis.variant
#
# category DIFFRN_SCAN_FRAME_MONITOR
#
# _diffrn_scan_frame_monitor.id
# _diffrn_scan_frame_monitor.detector_id
# _diffrn_scan_frame_monitor.scan_id
# _diffrn_scan_frame_monitor.frame_id
# _diffrn_scan_frame_monitor.integration_time
# _diffrn_scan_frame_monitor.monitor_value
# _diffrn_scan_frame_monitor.variant
#
# category MAP
#
# _map.details
# _map.diffrn_id
# _map.entry_id
# _map.id
# _map.variant
#
# category MAP_SEGMENT
#
# _map_segment.array_id
# _map_segment.array_section_id
# _map_segment.binary_id
# _map_segment.mask_array_id
# _map_segment.mask_array_section_id
# _map_segment.mask_binary_id
# _map_segment.id
# _map_segment.map_id
# _map_segment.details
# _map_segment.variant
#
# category VARIANT
#
# _variant.details
# _variant.diffrn_id
# _variant.entry_id
# _variant.role
# _variant.timestamp
# _variant.variant
# _variant.variant_of
#
# ***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
#
##############################################################################
ARRAY_DATA_GROUP
Categories that describe array data.
ARRAY_DATA
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.
ARRAY_ELEMENT_SIZE
Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
ARRAY_INTENSITIES
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.
ARRAY_STRUCTURE
Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
ARRAY_STRUCTURE_LIST
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.
ARRAY_STRUCTURE_LIST_SECTION
Data items in the ARRAY_STRUCTURE_LIST_SECTION category identify
the dimension-by-dimension start, end and stride of each section of an
array that is to be referenced.
For any array of array_id, ARRAYID, array section ids of the form
ARRAYID(start1:end1:stride1,start2:end2:stride2, ...)
are defined by default.
ARRAY_STRUCTURE_LIST_AXIS
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.
AXIS_GROUP
Categories that describe axes.
AXIS
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
DIFFRN_GROUP
Categories that describe details of the diffraction experiment.
DIFFRN_DATA_FRAME
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.
DIFFRN_DETECTOR
Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
DIFFRN_DETECTOR_AXIS
Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
DIFFRN_DETECTOR_ELEMENT
Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
DIFFRN_MEASUREMENT
Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
DIFFRN_MEASUREMENT_AXIS
Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
DIFFRN_RADIATION
Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
DIFFRN_REFLN
This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by _diffrn_refln.diffrn_id.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by _diffrn_reflns.diffrn_id and
_diffrn_refln.frame_id
DIFFRN_SCAN
Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
DIFFRN_SCAN_AXIS
Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
DIFFRN_SCAN_FRAME
Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
DIFFRN_SCAN_FRAME_AXIS
Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
DIFFRN_SCAN_FRAME_MONITOR
Data items in the DIFFRN_SCAN_FRAME_MONITOR category record
the values and details about each monitor for each frame of data
during a scan.
Each monitor value is uniquely identified by the combination of
the scan_id given by _diffrn_scan_frame.scan_id
the frame_id given by _diffrn_scan_frame_monitor.frame_id,
the monitor's detector_id given by
_diffrn_scan_frame_monitor.detector_id,
and a 1-based ordinal given by _diffrn_scan_frame_monitor.id.
If there is only one frame for the scan, the value of
_diffrn_scan_frame_monitor.frame_id may be
omitted.
A single frame may have more than one monitor value, and each
monitor value may be the result of integration over the entire
frame integration time given by the value of
_diffrn_scan_frame.integration_time
or many monitor values may be reported over shorter times given
by the value of _diffrn_scan_frame_monitor.integration_time. If
only one monitor value for a given monitor is collected during
the integration time of the frame, the value of
_diffrn_scan_frame_monitor.id may be
omitted.
MAP_GROUP
Categories that describe maps.
MAP
Data items in the MAP category record
the details of a maps. maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Examples are given in the MAP_SEGMENT category.
MAP_SEGMENT
Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
VARIANT_GROUP
Categories that describe variants
VARIANT
Data items in the VARIANT category record
the details about sets of variants of data items.
There is sometimes a need to allow for multiple versions of the
same data items in order to allow for refinements and corrections
to earlier assumptions, observations and calculations. In order
to allow data sets to contain more than one variant of the same
information, an optional ...variant data item as a pointer to
_variant.variant has been added to the key of every category,
as an implicit data item with a null (empty) default value.
All rows in a category with the same variant value are considered
to be related to one another and to all rows in other categories
with the same variant value. For a given variant, all such rows
are also considered to be related to all rows with a null variant
value, except that a row with a null variant value is for which
all other components of its key are identical to those entries
in another row with a non-null variant value is not related the
the rows with that non-null variant value. This behavior is
similar to the convention for identifying alternate conformers
in an atom list.
An optional role may be specified for a variant as the value of
_variant.role. Possible roles are null, "preferred",
"raw data", "unsuccessful trial".
variants may carry an optional timestamp as the value of
_variant.timestamp.
variants may be related to other variants from which they were
derived by the value of _variant.variant_of
Further details about the variant may be specified as the value
of _variant.details.
In order to allow variant information from multiple datasets to
be combined, _variant.diffrn_id and/or _variant.entry_id may
be used.
;
_dictionary.title cif_img.dic
_dictionary.version 1.7.10
_dictionary.datablock_id cif_img.dic
#########################
## 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.
;
'map_group'
'inclusive_group'
; Categories that describe details of map data.
;
'variant_group'
'inclusive_group'
; Categories that describe details of map data.
;
##################
## 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
_category.NX_mapping_details
;
_array_data.array_id ARRAYID
_array_data.binary_id BINARYID
_array_data.data DATAARRAY
_array_data.header_contents HEADER
_array_data.header_convention HEADERCONVENTION
-->
/CBF_diffrn_scan__SCANID:NXentry
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/data_ARRAYID_BINARYID=DATAARRAY
@CBF_array_id="ARRAYID"
@CBF_binary_id="BINARYID"
@CBF_header_contents="HEADER"
@CBF_header_convention="HEADERCONVENTION"
/data:NXdata
/data_ARRAYID_BINARYID-->
/CBF_diffrn_scan__SCANID/instrument/CBF_diffrn_detector__DETECTORNAME/data_ARRAYID_BINARYID
;
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
'_array_data.variant'
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_default.value 1
_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"'
or the parameter
'conversions="X-CBF_BACKGROUND_OFFSET_DELTA"'
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.
Note that the X-CBF_CANONICAL and X-CBF_PACKED are
slower but more efficient compressions that the others.
The X-CBF_BYTE_OFFSET compression is a good compromise
between speed and efficiency for ordinary diffraction
images. The X-CBF_BACKGROUND_OFFSET_DELTA compression
is oriented towards sparse data, such as masks and
tables of replacement pixel values for images with
overloaded spots.
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_
save__array_data.variant
_item_description.description
; The value of _array_data.variant gives the variant
to which the given ARRAY_DATA row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_data.variant'
_item.category_id array_data
_item.mandatory_code implicit
_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
_category.NX_mapping_details
;
_array_element_size.array_id ARRAYID
_array_element_size.index INDEX (See _array_element_size.array_id)
_array_element_size.size SIZE
-->
/entry:NXentry
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/?_pixel_size_ARRAYID=SIZE
@CBF_array_id="ARRAYID"
where "?" is "x", "y", "z" for
_array_element_size.index == 1,2, or 3 respectively
;
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
'_array_element_size.variant'
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 int
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_
save__array_element_size.variant
_item_description.description
; The value of _array_element_size.variant gives the variant
to which the given ARRAY_ELEMENT_SIZE row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_element_size.variant'
_item.category_id array_element_size
_item.mandatory_code implicit
_item_type.code code
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
_category.NX_mapping_details
;
_array_intensities.array_id ARRAYID
_array_intensities.binary_id BINARYID
_array_intensities.details DETAILS
_array_intensities.gain GAIN
_array_intensities.gain_esd GAINESD
_array_intensities.linearity LINEARITY
_array_intensities.offset OFFSET
_array_intensities.scaling SCALING
_array_intensities.overload OVERLOAD
_array_intensities.undefined_value UNDEFVAL
_array_intensities.pixel_fast_bin_size FBINSIZE
_array_intensities.pixel_slow_bin_size SBINSIZE
_array_intensities.pixel_binning_method METHOD
-->
/CBF_diffrn_scan__SCANID:NXentry
/data:NXdata
/data-->
/CBF_diffrn_scan__SCANID/instrument/CBF_diffrn_detector__DETECTORNAME/data_ARRAYID_BINARYID
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/data_ARRAYID_BINARYID=DATAARRAY
@CBF_array_id="ARRAYID"
@CBF_binary_id="BINARYID"
@details="DETAILS"
@gain=[GAIN]
@gain_esd=[GAINESD]
@linearity="LINEARITY"
@offset=[OFFSET]
@saturation_value=[OVERLOAD]
@scaling_factor=[SCALING]
@undefined_value=[UNDEFVAL]
@CBF_array_intensities__pixel_fast_bin_size=[FBINSIZE]
@CBF_array_intensities__pixel_slow_bin_size=[SBINSIZE]
@CBF_array_intensities__pixel_binning_method="METHOD"
The argument has been made that these attributes are not needed
because NeXus files are supposed to have "true values" stored.
In many cases that is true and then none of these attributes
are needed. However, with some detectors and some experiments
there are good technical and scientific reasons to bring in values
that will need processing later to derive "true values", and in
those case some or all of these attributes will be needed. They
are provided for such cases.
The same attributes could be used as fields in the case of a single
data array, but in that case links for all the fields would be needed
from NXdata to NXdetector, so it is preferable to use attributes even
in the case of a single data array. The reverse mapping will support
both uses.
;
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
'_array_intensities.variant'
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.details
_item_description.description
; A description of special aspects of the calculation of array intensities.
;
_item.name '_array_intensities.details'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code text
_item_examples.case 'Gain_setting: low gain (vrf = -0.300)'
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 of 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_
save__array_intensities.variant
_item_description.description
; The value of _array_intensities.variant gives the variant
to which the given ARRAY_INTENSITIES row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_intensities.variant'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
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.NX_mapping_details
;
Note that this is essentially a type that may apply to multiple
binary images, and corresponds to some of the detailed HDF5
information about an array. The following mapping is a placeholder
for the names given for future reference, if needed.
The information in this category is the byte order, the compression
information, and the encoding, which is carried in and reteievable
from the HDF5 types, properties lists, etc.
At present NeXus does not expose this information. This should be
discussed.
;
loop_
_category_key.name '_array_structure.id'
'_array_structure.variant'
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
;
'nibble_offset'
; Using the 'nibble_offset' compression scheme as per H. Bernstein
and the CBFlib manual, section 3.3.4
;
'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_structure_list_section.array_id' array_structure_list_section 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_structure_list_section.array_id'
'_array_structure.id'
'_array_intensities.array_id'
'_array_structure.id'
'_diffrn_data_frame.array_id'
'_array_structure.id'
save_
save__array_structure.variant
_item_description.description
; The value of _array_structure.variant gives the variant
to which the given ARRAY_STRUCTURE row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure.variant'
_item.category_id array_structure
_item.mandatory_code implicit
_item_type.code code
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
_category.NX_mapping_details
;
_array_structure_list.axis_set_id AXISSETID
_array_structure_list.array_id ARRAYID
_array_structure_list.dimension DIM
_array_structure_list.direction DIR
_array_structure_list.index INDEX
_array_structure_list.precedence PRECEDENCE
_array_structure_list_axis.axis_id AXISID
_array_structure_list_axis.axis_set_id AXISSETID
_array_structure_list_axis.angle ANGLE
_array_structure_list_axis.angle_increment ANGLEINC
_array_structure_list_axis.displacement DISP
_array_structure_list_axis.fract_displacement FRACTDISP
_array_structure_list_axis.displacement_increment DISPINC
_array_structure_list_axis.fract_displacement_increment FRACTINC
_array_structure_list_axis.angular_pitch ANGPITCH
_array_structure_list_axis.reference_angle REFANG
_array_structure_list_axis.reference_displacement REFDISP
-->
/CBF_diffrn_scan__SCANID:NXentry
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/CBF_array_structure_list_axis__AXISSETID=[]
@CBF_array_structure_list_axis__id="AXISSETID"
@CBF_array__id="ARRAYID"
@CBF_array_structure_list__dimension=DIM
@CBF_array_structure_list__direction="DIR"
@CBF_array_structure_list__index=INDEX
@CBF_array_structure_list__precedence=PRECEDENCE
/transformations:NXtransformations
/AXISID=[DISP,DISP+DISPINC,...] (or using angles where appropriate)
@depends_on=... determined from AXIS definitions
@equipment="detector"
@offset=[...] determined from AXIS definitions
@offset_units="mm"
@transformation_type="..." from AXIS definitions
@units="mm"
@vector=[...] determined from AXIS definitions
@CBF_array_structure_list_axis__axis_id="AXISID"
@CBF_array_structure_list_axis__axis_set_id="AXISSETID"
@CBF_array_structure_list_axis__angle=ANGLE
@CBF_array_structure_list_axis__angle_increment=ANGLEINC
@CBF_array_structure_list_axis__displacement=DISP
@CBF_array_structure_list_axis__displacement=FRACTDISP
@CBF_array_structure_list_axis__displacement_increment=DISPINC
@CBF_array_structure_list_axis__fract_displacement_increment=FRACTINC
@CBF_array_structure_list_axis__angular_pitch=ANGPITCH
@CBF_array_structure_list_axis__radial_pitch=RADPITCH
@CBF_array_structure_list_axis__reference_angle=REFANG
@CBF_array_structure_list_axis__reference_displacement=REFDISP
with the parent category for the axis set and axis determined by the equipment
of the axes.
;
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
'_array_structure_list.variant'
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_structure_list_section.index'
'_array_structure_list.index'
'_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_
save__array_structure_list.variant
_item_description.description
; The value of _array_structure_list.variant gives the variant
to which the given ARRAY_STRUCTURE_LIST row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure_list.variant'
_item.category_id array_structure_list
_item.mandatory_code implicit
_item_type.code code
save_
################################
# ARRAY_STRUCTURE_LIST_SECTION #
################################
save_array_structure_list_section
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_SECTION category identify
the dimension-by-dimension start, end and stride of each section of an
array that is to be referenced.
For any array of array_id, ARRAYID, array section ids of the form
ARRAYID(start1:end1:stride1,start2:end2:stride2, ...) are defined
by default.
For the given index, the elements in
the section are of indices: _array_structure_list_section.start,
_array_structure_list_section.start
+_array_structure_list_section.stride,
_array_structure_list_section.start
+2*_array_structure_list_section.stride,
...
stopping either when the indices leave the limits of the indices of that dimension
or [min(_array_structure_list_section.start,
_array_structure_list_section.end),
max(_array_structure_list_section.start,
_array_structure_list_section.end)].
The ordering of these elements is determined by the overall ordering of
_array_structure_list_section.array_id and not by the ordering implied by the
stride.
;
_category.id array_structure_list_section
_category.mandatory_code no
_category.NX_mapping_details
;
_array_structure_list_section.array_id ARRAYID -->
_array_structure_list_section.id SECTIONID -->
_array_structure_list_section.index INDEX-->
_array_structure_list_section.end END -->
_array_structure_list_section.start START -->
_array_structure_list_section.stride STRIDE -->
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/CBF_array_structure_list_section__SECTIONID=[]
@CBF_array_structure_list_section__index=INDEX
@CBF_array_structure_list_section__end=END
@CBF_array_structure_list_section__start=START
@CBF_array_structure_list_section__stride=STRIDE
;
loop_
_category_key.name '_array_structure_list_section.id'
'_array_structure_list_section.array_id'
'_array_structure_list_section.index'
'_array_structure_list_section.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array, myarry, of 1300 x 1200 elements,
700 frames is defined in ARRAY_STRUCTURE_LIST, and
the array section identifier
"myarray(101:1200,101:1100,1:700:10)"
is explicitly defined taking every 10th frame and
removing a 100 pixel border. Note that even though
the slow index high is 700, the last frame that
will actually be included in only 691.
;
;
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
myarray 1 1300 1 increasing ELEMENT_X
myarray 2 1200 2 increasing ELEMENT_Y
myarray 3 700 3 increasing FRAME_NO
loop_
_array_structure_list_section.id
_array_structure_list_section.array_id
_array_structure_list_section.index
_array_structure_list_section.start
_array_structure_list_section.end
_array_structure_list_section.stride
"myarray(101:1200,101:1100,1:700:10)" myarray 1 101 1200 .
"myarray(101:1200,101:1100,1:700:10)" myarray 2 101 1100 .
"myarray(101:1200,101:1100,1:700:10)" myarray 3 1 700 10
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list_section.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list_section.array_id'
_item.category_id array_structure_list_section
_item.mandatory_code mandatory
_item_type.code code
save_
save__array_structure_list_section.end
_item_description.description
; Identifies the ending ordinal, numbered from 1, for an array
element of index _array_structure_list_section.index in the
section.
The value defaults to the dimension for index
_array_structure_list_section.index
of the array.
Note that this agrees with the Fortran convention, rather than
the Python convention in that, if compatible with the stride,
the end element is included in the section as in Fortran, rather
than being one beyond the section as in Python.
;
_item.name '_array_structure_list_section.end'
_item.category_id array_structure_list_section
_item.mandatory_code implicit
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list_section.id
_item_description.description
; Uniquely identifies the array section chosen.
To avoid confusion array section IDs that contain parentheses
should conform to the default syntax
ARRAYID(start1:end1:stride1,start2:end2:stride2, ...)
;
_item.name '_array_structure_list_section.id'
_item.category_id array_structure_list_section
_item.mandatory_code yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.array_section_id'
'_array_structure_list_section.id'
'_map_segment.array_section_id'
'_array_structure_list_section.id'
save_
save__array_structure_list_section.index
_item_description.description
; This item is a pointer to _array_structure_list.index
in the ARRAY_STRUCTURE_LIST category.
Identifies the one-based index of the row, column, sheet ...
the ARRAY_STRUCTURE_LIST category.
For a multidimensional array, a value must be explicitly given.
If an index is omitted from section then all elements for that
index are assumed to be included in the section.
;
_item.name '_array_structure_list_section.index'
_item.category_id array_structure_list_section
_item.mandatory_code implicit
_item_type.code int
save_
save__array_structure_list_section.start
_item_description.description
; Identifies the starting ordinal, numbered from 1,
for an array element of index _array_structure_list_section.index
in the section.
The value defaults to 1. For the given index, the elements in
the section are of indices: _array_structure_list_section.start,
_array_structure_list_section.start
+_array_structure_list_section.stride,
_array_structure_list_section.start
+2*_array_structure_list_section.stride,
...
stopping either when the indices leave the limits of the indices of that dimension
or [min(_array_structure_list_section.start,
_array_structure_list_section.end),
max(_array_structure_list_section.start,
_array_structure_list_section.end)].
The ordering of these elements is determined by the overall ordering of
_array_structure_list_section.array_id and not by the ordering implied by the
stride.
;
_item.name '_array_structure_list_section.start'
_item.category_id array_structure_list_section
_item.mandatory_code implicit
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list_section.stride
_item_description.description
; Identifies the incremental steps to be taken when moving
element to element in the section in that particular
dimension. The value of _array_structure_list_section.stride may be
positive or negative. If the stride is zero, the section is
just defined by _array_structure_list_section.start.
;
_item.name '_array_structure_list_section.stride'
_item.category_id array_structure_list_section
_item.mandatory_code no
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list_section.variant
_item_description.description
; The value of _array_structure_list_section.variant gives the variant
to which the given ARRAY_STRUCTURE_LIST_SECTION row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure_list_section.variant'
_item.category_id array_structure_list_section
_item.mandatory_code implicit
_item_type.code code
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
_category.NX_mapping_details
;
_array_structure_list.axis_set_id AXISSETID
_array_structure_list.array_id ARRAYID
_array_structure_list.dimension DIM
_array_structure_list.direction DIR
_array_structure_list.index INDEX
_array_structure_list.precedence PRECEDENCE
_array_structure_list_axis.axis_id AXISID
_array_structure_list_axis.axis_set_id AXISSETID
_array_structure_list_axis.angle ANGLE
_array_structure_list_axis.angle_increment ANGLEINC
_array_structure_list_axis.displacement DISP
_array_structure_list_axis.fract_displacement FRACTDISP
_array_structure_list_axis.displacement_increment DISPINC
_array_structure_list_axis.fract_displacement_increment FRACTINC
_array_structure_list_axis.angular_pitch ANGPITCH
_array_structure_list_axis.reference_angle REFANG
_array_structure_list_axis.reference_displacement REFDISP
-->
/CBF_diffrn_scan__SCANID:NXentry
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/CBF_array_structure_list_axis__AXISSETID=[]
@CBF_array_structure_list_axis__id="AXISSETID"
@CBF_array__id="ARRAYID"
@CBF_array_structure_list__dimension=DIM
@CBF_array_structure_list__direction="DIR"
@CBF_array_structure_list__index=INDEX
@CBF_array_structure_list__precedence=PRECEDENCE
/transformations:NXtransformations
/AXISID=[DISP,DISP+DISPINC,...] (or using angles where appropriate)
@depends_on=... determined from AXIS definitions
@equipment="detector"
@offset=[...] determined from AXIS definitions
@offset_units="mm"
@transformation_type="..." from AXIS definitions
@units="mm"
@vector=[...] determined from AXIS definitions
@CBF_array_structure_list_axis__axis_id="AXISID"
@CBF_array_structure_list_axis__axis_set_id="AXISSETID"
@CBF_array_structure_list_axis__angle=ANGLE
@CBF_array_structure_list_axis__angle_increment=ANGLEINC
@CBF_array_structure_list_axis__displacement=DISP
@CBF_array_structure_list_axis__displacement=FRACTDISP
@CBF_array_structure_list_axis__displacement_increment=DISPINC
@CBF_array_structure_list_axis__fract_displacement_increment=FRACTINC
@CBF_array_structure_list_axis__angular_pitch=ANGPITCH
@CBF_array_structure_list_axis__radial_pitch=RADPITCH
@CBF_array_structure_list_axis__reference_angle=REFANG
@CBF_array_structure_list_axis__reference_displacement=REFDISP
with the parent category for the axis set and axis determined by the equipment
of the axes.
;
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
'_array_structure_list_axis.variant'
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_axis.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_axis.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_
save__array_structure_list_axis.variant
_item_description.description
; The value of _array_structure_list_axis.variant gives the variant
to which the given ARRAY_STRUCTURE_LIST_AXIS row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_array_structure_list_axis.variant'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
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.
For convenience when describing detector element (module) placement,
and optional mounting rotation axis and rotation angle may be
specified. In such cases, the mounting rotation axis and angle
of rotation around the mounting rotation axis are applied after
applying the transformations upon which the given axis depends.
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
_category.NX_mapping_details
;
_axis.id AXISID
_axis.type AXISTYPE
_axis.equipment AXISEQUIPMENT
_axis.equipment_component AXISEQUIPCOMP
_axis.depends_on AXISDEPENDSON
_axis.rotation_axis AXISROTAXIS
_axis.rotation AXISROTATION
_axis.vector[1] AXISV1
_axis.vector[2] AXISV2
_axis.vector[3] AXISV3
_axis.offset[1] AXISO1
_axis.offset[2] AXISO2
_axis.offset[3] AXISO3
_axis.system AXISSYSTEM
-->
{ /CBF_diffrn_scan__SCANID:NXentry
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
for AXISEQUIPMENT=="detector"}
{ /CBF_diffrn_scan__SCANID:NXentry
/sample:NXsample
for AXISEQUIPMENT=="goniometer"}
{ /CBF_diffrn_scan__SCANID:NXentry
/coordinate_system:NXcoordinate_system
for AXISEQUIPMENT=="general"}
/transformations:NXtransformations
/AXISID=[]
@units="mm" if AXISTYPE=="translation"
or @units="degrees" if AXISTYPE=="rotation"
@transformation_type="AXISTYPE"
@equipment_component="AXISEQUIPCOMP"
@depends_on="AXISDEPENDSON"
@rotation_axis="AXISROTAXIS"
@rotation=AXISROTATION
@rotation_units="degrees"
@offset=offsetxform([O1,O2,O3])
@offset_inits="mm"
@vector=coordxform([V1,V2,V3])
Differences in Coordinate Frames
The standard coordinate frame in NeXus is the McStas coordinate frame,
in which the Z-axis points in the direction of the incident beam, the
X-axis is orthogonal to the Z-axis in the horizontal plane and pointing
left as seen from the source and the Y-axis points upwards. The
origin is in the sample.
The standard coordinate frame in imgCIF/CBF aligns the X-axis to the
principal goniometer axis, chooses the Z-axis to point from the sample
into the beam. If the beam is not orthogonal to the X-axis, the Z-axis
is the component of the vector points into the beam orthogonal to the
X-axis. The Y-axis is chosen to complete a right-handed axis system.
Let us call the NeXus coordinate axes, X_nx, Y_nx and Z_nx and the
imgCIF/CBF coordinate axes, X_cbf, Y_cbf and $Z_cbf and the direction
of gravity, Gravity. In order to translate a vector v_nx = ( x, y, z)
from the NeXus coordinate system to the imgCIF coordinate system, we
also need two additional axes, as unit vectors, Gravity_cbf the downwards
direction, and Beam_cbf, the direction of the beam e.g. ( 0, 0, -1)).
In practice, the beam is not necessarily perfectly horizontal, so Y_nx
is not necessarily perfectly vertical. Therefore, in order to generate
X_nx, Y_nx and Z_nx some care is needed. The cross product between two
vectors a and b is a new vector c orthogonal to both a and b,
chosen so that a, b, c is a right handed system. If a and b are
orthogonal unit vectors, this right-handed system is an orthonormal
coordinate system.
In the CBF coordinate frame, Z_nx is aligned to Beam_cbf
Z_nx = Beam_cbf
X_nx is defined as being horizontal at right angles to the beam,
pointing to the left when seen from the source. Assuming the beam is
not vertical, we can compute X_nx as the normalized cross product of
the beam and the gravity:
X_nx = (Beam_cbf x Gravity_cbf)/||Beam_cbf x Gravity_cbf||
To see that this satisfies the constraint of being horizontal and
pointing to the left, consider the case of Beam = ( 0, 0, -1 )
and Gravity = ( 0, 0, 1 ) then we would have X_nx = ( 1, 0, 0 )
from the cross product above. The normalization is only necessary
if the beam is not horizontal.
Finally Y_nx is computed as the cross product of the beam and X_nx,
completing an orthonormal right-handed system with Y_nx pointing upwards
Y_nx = Beam_cbf x X_nx
Then we know that in the imgCIF/CBF coordinate frame
v_nx = X.X_nx + Y.Y_nx + Z.Z_nx
Thus, given the imgCIF/CBF vectors for the true direction of the beam
and the true direction of gravity, we have a linear transformation from
the NeXus coordinate frame to the imgCIF/CBF coordinate frame. The
origins of the two frames agree. The inverse linear transformation will
transform a vector in the imgCIF/CBF coordinate frame into the NeXus
coordinate frame.
In the common case in which the beam is orthogonal to the principal
goniometer axis so that Beam_cbf = ( 0, 0, -1 ) and the imgCIF/CBF
Y-axis points upwards, the transformation inverts the X and Z axes.
In the other common case in which the beam is orthogonal to the
principal goniometer axis and the imgCIF/CBF Y-axis points
downwards, the transformation inverts the Y and Z axes.
mapping Axes
There are two transformations needed: coordxform(v) which takes a vector,
v, the the CBF imgCIF Standard Laboratory Coordinate System and returns the
equivalent McStas coordinate vector, and offsetxform(o) which takes an
offset, o, in the the CBF imgCIF Standard Laboratory Coordinate System and
returns the equivalent NeXus offset. As of this writing, it has not
been decided as to whether the NeXus offset should also be relative
(in which case offsetxform = coordxform) or whether the NeXus offset should
be absolute.
In imgCIF/CBF all the information about all axes other than their
settings are gathered in one AXIS category. The closest equivalent
container in NeXus is the NXinstrument class. We put the information
about detector axes into an detector:NXdetector NeXus class instance,
information about the goniometer into an goniometer:NXgoniometer NeXus
class instance, etc. Additionally, in view of the general nature of
some axes, such as the coordinate frame axes and gravity, we add a
coordinate_system:NXcoordinate_system NeXus class instance with
axis__gravity, axis__beam and other axes not tied to specific equipment.
We have applied the coordinate frame transformation changing
the CBF laboratory coordinates into McStas coordinates. Notice that X and
Z have changed direction, but Y has not. In other experimental setup,
other transformations may occur. The offsets for dependent axes are
given relative to the total offset of axes on which that axis is dependent.
Note that the axis settings do not enter into this calculation, because the
offsets of dependent axes are given with all axes at their zero settings
The cbf_location attribute gives a mapping back into the CBF AXIS category
in dotted notation. The first component is the data block. The second
component is "axis". The third component is either "vector" or
"offset" for information drawn from the AXIS.VECTOR[...] or
AXIS.OFFSET[...] respectively. The last component is the CBF row number
to facilitate recovering the original CBF layout.
;
loop_
_category_key.name '_axis.id'
'_axis.equipment'
'_axis.variant'
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_set_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_set_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
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 5 -
This example show an excerpt from the axis specification of an FEL detector
provided by N. Sauter and A. Brewster.
The detector is divided into 4 quadrants, each quadrant contains 8 sensors
and each sensor contains 2 ASICs. We want to be able to refine the
placement of each of these elements, so we maintain the set of vectors
that places them.
;
;
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
CSPAD_FRONT AXIS_D0_X
CSPAD_FRONT AXIS_D0_Y
CSPAD_FRONT AXIS_D0_Z
CSPAD_FRONT AXIS_D0_R
CSPAD_FRONT FS_D0Q0
CSPAD_FRONT FS_D0Q0S0
CSPAD_FRONT FS_D0Q0S0A0
CSPAD_FRONT FS_D0Q0S0A1
CSPAD_FRONT FS_D0Q0S1
CSPAD_FRONT FS_D0Q0S1A0
CSPAD_FRONT FS_D0Q0S1A1
CSPAD_FRONT FS_D0Q0S2
CSPAD_FRONT FS_D0Q0S2A0
CSPAD_FRONT FS_D0Q0S2A1
CSPAD_FRONT FS_D0Q0S3
CSPAD_FRONT FS_D0Q0S3A0
CSPAD_FRONT FS_D0Q0S3A1
CSPAD_FRONT FS_D0Q0S4
CSPAD_FRONT FS_D0Q0S4A0
CSPAD_FRONT FS_D0Q0S4A1
CSPAD_FRONT FS_D0Q0S5
CSPAD_FRONT FS_D0Q0S5A0
CSPAD_FRONT FS_D0Q0S5A1
CSPAD_FRONT FS_D0Q0S6
CSPAD_FRONT FS_D0Q0S6A0
CSPAD_FRONT FS_D0Q0S6A1
CSPAD_FRONT FS_D0Q0S7
CSPAD_FRONT FS_D0Q0S7A0
CSPAD_FRONT FS_D0Q0S7A1
CSPAD_FRONT FS_D0Q1
CSPAD_FRONT FS_D0Q1S0
CSPAD_FRONT FS_D0Q1S0A0
CSPAD_FRONT FS_D0Q1S0A1
CSPAD_FRONT FS_D0Q1S1
CSPAD_FRONT FS_D0Q1S1A0
CSPAD_FRONT FS_D0Q1S1A1
CSPAD_FRONT FS_D0Q1S2
CSPAD_FRONT FS_D0Q1S2A0
CSPAD_FRONT FS_D0Q1S2A1
CSPAD_FRONT FS_D0Q1S3
CSPAD_FRONT FS_D0Q1S3A0
CSPAD_FRONT FS_D0Q1S3A1
CSPAD_FRONT FS_D0Q1S4
CSPAD_FRONT FS_D0Q1S4A0
CSPAD_FRONT FS_D0Q1S4A1
CSPAD_FRONT FS_D0Q1S5
CSPAD_FRONT FS_D0Q1S5A0
CSPAD_FRONT FS_D0Q1S5A1
CSPAD_FRONT FS_D0Q1S6
CSPAD_FRONT FS_D0Q1S6A0
CSPAD_FRONT FS_D0Q1S6A1
CSPAD_FRONT FS_D0Q1S7
CSPAD_FRONT FS_D0Q1S7A0
CSPAD_FRONT FS_D0Q1S7A1
CSPAD_FRONT FS_D0Q2
CSPAD_FRONT FS_D0Q2S0
CSPAD_FRONT FS_D0Q2S0A0
CSPAD_FRONT FS_D0Q2S0A1
CSPAD_FRONT FS_D0Q2S1
CSPAD_FRONT FS_D0Q2S1A0
CSPAD_FRONT FS_D0Q2S1A1
CSPAD_FRONT FS_D0Q2S2
CSPAD_FRONT FS_D0Q2S2A0
CSPAD_FRONT FS_D0Q2S2A1
CSPAD_FRONT FS_D0Q2S3
CSPAD_FRONT FS_D0Q2S3A0
CSPAD_FRONT FS_D0Q2S3A1
CSPAD_FRONT FS_D0Q2S4
CSPAD_FRONT FS_D0Q2S4A0
CSPAD_FRONT FS_D0Q2S4A1
CSPAD_FRONT FS_D0Q2S5
CSPAD_FRONT FS_D0Q2S5A0
CSPAD_FRONT FS_D0Q2S5A1
CSPAD_FRONT FS_D0Q2S6
CSPAD_FRONT FS_D0Q2S6A0
CSPAD_FRONT FS_D0Q2S6A1
CSPAD_FRONT FS_D0Q2S7
CSPAD_FRONT FS_D0Q2S7A0
CSPAD_FRONT FS_D0Q2S7A1
CSPAD_FRONT FS_D0Q3
CSPAD_FRONT FS_D0Q3S0
CSPAD_FRONT FS_D0Q3S0A0
CSPAD_FRONT FS_D0Q3S0A1
CSPAD_FRONT FS_D0Q3S1
CSPAD_FRONT FS_D0Q3S1A0
CSPAD_FRONT FS_D0Q3S1A1
CSPAD_FRONT FS_D0Q3S2
CSPAD_FRONT FS_D0Q3S2A0
CSPAD_FRONT FS_D0Q3S2A1
CSPAD_FRONT FS_D0Q3S3
CSPAD_FRONT FS_D0Q3S3A0
CSPAD_FRONT FS_D0Q3S3A1
CSPAD_FRONT FS_D0Q3S4
CSPAD_FRONT FS_D0Q3S4A0
CSPAD_FRONT FS_D0Q3S4A1
CSPAD_FRONT FS_D0Q3S5
CSPAD_FRONT FS_D0Q3S5A0
CSPAD_FRONT FS_D0Q3S5A1
CSPAD_FRONT FS_D0Q3S6
CSPAD_FRONT FS_D0Q3S6A0
CSPAD_FRONT FS_D0Q3S6A1
CSPAD_FRONT FS_D0Q3S7
CSPAD_FRONT FS_D0Q3S7A0
CSPAD_FRONT FS_D0Q3S7A1
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELE_D0Q0S0A0 CSPAD_FRONT
ELE_D0Q0S0A1 CSPAD_FRONT
ELE_D0Q0S1A0 CSPAD_FRONT
ELE_D0Q0S1A1 CSPAD_FRONT
ELE_D0Q0S2A0 CSPAD_FRONT
ELE_D0Q0S2A1 CSPAD_FRONT
ELE_D0Q0S3A0 CSPAD_FRONT
ELE_D0Q0S3A1 CSPAD_FRONT
ELE_D0Q0S4A0 CSPAD_FRONT
ELE_D0Q0S4A1 CSPAD_FRONT
ELE_D0Q0S5A0 CSPAD_FRONT
ELE_D0Q0S5A1 CSPAD_FRONT
ELE_D0Q0S6A0 CSPAD_FRONT
ELE_D0Q0S6A1 CSPAD_FRONT
ELE_D0Q0S7A0 CSPAD_FRONT
ELE_D0Q0S7A1 CSPAD_FRONT
ELE_D0Q1S0A0 CSPAD_FRONT
ELE_D0Q1S0A1 CSPAD_FRONT
ELE_D0Q1S1A0 CSPAD_FRONT
ELE_D0Q1S1A1 CSPAD_FRONT
ELE_D0Q1S2A0 CSPAD_FRONT
ELE_D0Q1S2A1 CSPAD_FRONT
ELE_D0Q1S3A0 CSPAD_FRONT
ELE_D0Q1S3A1 CSPAD_FRONT
ELE_D0Q1S4A0 CSPAD_FRONT
ELE_D0Q1S4A1 CSPAD_FRONT
ELE_D0Q1S5A0 CSPAD_FRONT
ELE_D0Q1S5A1 CSPAD_FRONT
ELE_D0Q1S6A0 CSPAD_FRONT
ELE_D0Q1S6A1 CSPAD_FRONT
ELE_D0Q1S7A0 CSPAD_FRONT
ELE_D0Q1S7A1 CSPAD_FRONT
ELE_D0Q2S0A0 CSPAD_FRONT
ELE_D0Q2S0A1 CSPAD_FRONT
ELE_D0Q2S1A0 CSPAD_FRONT
ELE_D0Q2S1A1 CSPAD_FRONT
ELE_D0Q2S2A0 CSPAD_FRONT
ELE_D0Q2S2A1 CSPAD_FRONT
ELE_D0Q2S3A0 CSPAD_FRONT
ELE_D0Q2S3A1 CSPAD_FRONT
ELE_D0Q2S4A0 CSPAD_FRONT
ELE_D0Q2S4A1 CSPAD_FRONT
ELE_D0Q2S5A0 CSPAD_FRONT
ELE_D0Q2S5A1 CSPAD_FRONT
ELE_D0Q2S6A0 CSPAD_FRONT
ELE_D0Q2S6A1 CSPAD_FRONT
ELE_D0Q2S7A0 CSPAD_FRONT
ELE_D0Q2S7A1 CSPAD_FRONT
ELE_D0Q3S0A0 CSPAD_FRONT
ELE_D0Q3S0A1 CSPAD_FRONT
ELE_D0Q3S1A0 CSPAD_FRONT
ELE_D0Q3S1A1 CSPAD_FRONT
ELE_D0Q3S2A0 CSPAD_FRONT
ELE_D0Q3S2A1 CSPAD_FRONT
ELE_D0Q3S3A0 CSPAD_FRONT
ELE_D0Q3S3A1 CSPAD_FRONT
ELE_D0Q3S4A0 CSPAD_FRONT
ELE_D0Q3S4A1 CSPAD_FRONT
ELE_D0Q3S5A0 CSPAD_FRONT
ELE_D0Q3S5A1 CSPAD_FRONT
ELE_D0Q3S6A0 CSPAD_FRONT
ELE_D0Q3S6A1 CSPAD_FRONT
ELE_D0Q3S7A0 CSPAD_FRONT
ELE_D0Q3S7A1 CSPAD_FRONT
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]
_axis.equipment_component
_axis.rotation
_axis.rotation_axis
AXIS_SOURCE general source . 0 0 1 . . . . . .
AXIS_GRAVITY general gravity . 0 -1 0 . . . . . .
AXIS_D0_Z translation detector . 0 0 1 . . . detector_arm . .
AXIS_D0_Y translation detector AXIS_D0_Z 0 1 0 . . . detector_arm . .
AXIS_D0_X translation detector AXIS_D0_Y 1 0 0 . . . detector_arm . .
AXIS_D0_R rotation detector AXIS_D0_X 0 0 1 0.0 0.0 0.0 detector_arm . .
FS_D0Q0 rotation detector AXIS_D0_R 0 0 1 -49.860765625 41.643353125 0.0 detector_quadrant . .
FS_D0Q0S0 rotation detector FS_D0Q0 0.0 0.0 1.0 11.3696 -23.189925 0.0 detector_sensor . .
FS_D0Q0S0A0 rotation detector FS_D0Q0S0 0 0 1 -10.835 0.0 0.0 detector_asic 89.66181 FS_D0Q0S0
AXIS_D0Q0S0A0_F translation detector FS_D0Q0S0A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S0A0_S translation detector AXIS_D0Q0S0A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S0A1 rotation detector FS_D0Q0S0 0 0 1 10.835 0.0 0.0 detector_asic 89.66181 FS_D0Q0S0
AXIS_D0Q0S0A1_F translation detector FS_D0Q0S0A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S0A1_S translation detector AXIS_D0Q0S0A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S1 rotation detector FS_D0Q0 0.0 0.0 1.0 34.815 -23.309825 0.0 detector_sensor . .
FS_D0Q0S1A0 rotation detector FS_D0Q0S1 0 0 1 -10.835 0.0 0.0 detector_asic 90.00132 FS_D0Q0S1
AXIS_D0Q0S1A0_F translation detector FS_D0Q0S1A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S1A0_S translation detector AXIS_D0Q0S1A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S1A1 rotation detector FS_D0Q0S1 0 0 1 10.835 0.0 0.0 detector_asic 90.00132 FS_D0Q0S1
AXIS_D0Q0S1A1_F translation detector FS_D0Q0S1A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S1A1_S translation detector AXIS_D0Q0S1A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S2 rotation detector FS_D0Q0 -0.0 -0.0 -1.0 -23.5389 -10.921625 0.0 detector_sensor . .
FS_D0Q0S2A0 rotation detector FS_D0Q0S2 0 0 1 -10.835 0.0 0.0 detector_asic 359.68548 FS_D0Q0S2
AXIS_D0Q0S2A0_F translation detector FS_D0Q0S2A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S2A0_S translation detector AXIS_D0Q0S2A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S2A1 rotation detector FS_D0Q0S2 0 0 1 10.835 0.0 0.0 detector_asic 359.68548 FS_D0Q0S2
AXIS_D0Q0S2A1_F translation detector FS_D0Q0S2A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S2A1_S translation detector AXIS_D0Q0S2A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S3 rotation detector FS_D0Q0 0.0 0.0 1.0 -23.5499 -34.181125 0.0 detector_sensor . .
FS_D0Q0S3A0 rotation detector FS_D0Q0S3 0 0 1 -10.835 0.0 0.0 detector_asic 359.96513 FS_D0Q0S3
AXIS_D0Q0S3A0_F translation detector FS_D0Q0S3A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S3A0_S translation detector AXIS_D0Q0S3A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S3A1 rotation detector FS_D0Q0S3 0 0 1 10.835 0.0 0.0 detector_asic 359.96513 FS_D0Q0S3
AXIS_D0Q0S3A1_F translation detector FS_D0Q0S3A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S3A1_S translation detector AXIS_D0Q0S3A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S4 rotation detector FS_D0Q0 0.0 0.0 1.0 -11.2651 24.282775 0.0 detector_sensor . .
FS_D0Q0S4A0 rotation detector FS_D0Q0S4 0 0 1 -10.835 0.0 0.0 detector_asic 270.14738 FS_D0Q0S4
AXIS_D0Q0S4A0_F translation detector FS_D0Q0S4A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S4A0_S translation detector AXIS_D0Q0S4A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S4A1 rotation detector FS_D0Q0S4 0 0 1 10.835 0.0 0.0 detector_asic 270.14738 FS_D0Q0S4
AXIS_D0Q0S4A1_F translation detector FS_D0Q0S4A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S4A1_S translation detector AXIS_D0Q0S4A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S5 rotation detector FS_D0Q0 0.0 0.0 1.0 -34.7336 24.169475 0.0 detector_sensor . .
FS_D0Q0S5A0 rotation detector FS_D0Q0S5 0 0 1 -10.835 0.0 0.0 detector_asic 270.07896 FS_D0Q0S5
AXIS_D0Q0S5A0_F translation detector FS_D0Q0S5A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S5A0_S translation detector AXIS_D0Q0S5A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S5A1 rotation detector FS_D0Q0S5 0 0 1 10.835 0.0 0.0 detector_asic 270.07896 FS_D0Q0S5
AXIS_D0Q0S5A1_F translation detector FS_D0Q0S5A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S5A1_S translation detector AXIS_D0Q0S5A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S6 rotation detector FS_D0Q0 0.0 0.0 1.0 23.5488 33.320375 0.0 detector_sensor . .
FS_D0Q0S6A0 rotation detector FS_D0Q0S6 0 0 1 -10.835 0.0 0.0 detector_asic 359.78222 FS_D0Q0S6
AXIS_D0Q0S6A0_F translation detector FS_D0Q0S6A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S6A0_S translation detector AXIS_D0Q0S6A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S6A1 rotation detector FS_D0Q0S6 0 0 1 10.835 0.0 0.0 detector_asic 359.78222 FS_D0Q0S6
AXIS_D0Q0S6A1_F translation detector FS_D0Q0S6A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S6A1_S translation detector AXIS_D0Q0S6A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S7 rotation detector FS_D0Q0 0.0 0.0 1.0 23.3541 9.829875 0.0 detector_sensor . .
FS_D0Q0S7A0 rotation detector FS_D0Q0S7 0 0 1 -10.835 0.0 0.0 detector_asic 359.89604 FS_D0Q0S7
AXIS_D0Q0S7A0_F translation detector FS_D0Q0S7A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S7A0_S translation detector AXIS_D0Q0S7A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q0S7A1 rotation detector FS_D0Q0S7 0 0 1 10.835 0.0 0.0 detector_asic 359.89604 FS_D0Q0S7
AXIS_D0Q0S7A1_F translation detector FS_D0Q0S7A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q0S7A1_S translation detector AXIS_D0Q0S7A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1 rotation detector AXIS_D0_R 0 0 1 41.512521875 50.149653125 0.0 detector_quadrant . .
FS_D0Q1S0 rotation detector FS_D0Q1 -0.0 -0.0 -1.0 -23.1589875 -11.451825 0.0 detector_sensor . .
FS_D0Q1S0A0 rotation detector FS_D0Q1S0 0 0 1 -10.835 0.0 0.0 detector_asic 0.27238 FS_D0Q1S0
AXIS_D0Q1S0A0_F translation detector FS_D0Q1S0A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S0A0_S translation detector AXIS_D0Q1S0A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S0A1 rotation detector FS_D0Q1S0 0 0 1 10.835 0.0 0.0 detector_asic 0.27238 FS_D0Q1S0
AXIS_D0Q1S0A1_F translation detector FS_D0Q1S0A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S0A1_S translation detector AXIS_D0Q1S0A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S1 rotation detector FS_D0Q1 -0.0 -0.0 -1.0 -23.2073875 -34.782825 0.0 detector_sensor . .
FS_D0Q1S1A0 rotation detector FS_D0Q1S1 0 0 1 -10.835 0.0 0.0 detector_asic 0.00525999986641 FS_D0Q1S1
AXIS_D0Q1S1A0_F translation detector FS_D0Q1S1A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S1A0_S translation detector AXIS_D0Q1S1A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S1A1 rotation detector FS_D0Q1S1 0 0 1 10.835 0.0 0.0 detector_asic 0.00525999986641 FS_D0Q1S1
AXIS_D0Q1S1A1_F translation detector FS_D0Q1S1A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S1A1_S translation detector AXIS_D0Q1S1A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S2 rotation detector FS_D0Q1 0.0 0.0 1.0 -10.7311875 23.286175 0.0 detector_sensor . .
FS_D0Q1S2A0 rotation detector FS_D0Q1S2 0 0 1 -10.835 0.0 0.0 detector_asic 270.02545 FS_D0Q1S2
AXIS_D0Q1S2A0_F translation detector FS_D0Q1S2A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S2A0_S translation detector AXIS_D0Q1S2A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S2A1 rotation detector FS_D0Q1S2 0 0 1 10.835 0.0 0.0 detector_asic 270.02545 FS_D0Q1S2
AXIS_D0Q1S2A1_F translation detector FS_D0Q1S2A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S2A1_S translation detector AXIS_D0Q1S2A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S3 rotation detector FS_D0Q1 0.0 0.0 1.0 -34.1402875 23.344475 0.0 detector_sensor . .
FS_D0Q1S3A0 rotation detector FS_D0Q1S3 0 0 1 -10.835 0.0 0.0 detector_asic 270.03066 FS_D0Q1S3
AXIS_D0Q1S3A0_F translation detector FS_D0Q1S3A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S3A0_S translation detector AXIS_D0Q1S3A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S3A1 rotation detector FS_D0Q1S3 0 0 1 10.835 0.0 0.0 detector_asic 270.03066 FS_D0Q1S3
AXIS_D0Q1S3A1_F translation detector FS_D0Q1S3A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S3A1_S translation detector AXIS_D0Q1S3A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S4 rotation detector FS_D0Q1 0.0 0.0 1.0 24.0035125 11.407275 0.0 detector_sensor . .
FS_D0Q1S4A0 rotation detector FS_D0Q1S4 0 0 1 -10.835 0.0 0.0 detector_asic 179.96381 FS_D0Q1S4
AXIS_D0Q1S4A0_F translation detector FS_D0Q1S4A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S4A0_S translation detector AXIS_D0Q1S4A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S4A1 rotation detector FS_D0Q1S4 0 0 1 10.835 0.0 0.0 detector_asic 179.96381 FS_D0Q1S4
AXIS_D0Q1S4A1_F translation detector FS_D0Q1S4A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S4A1_S translation detector AXIS_D0Q1S4A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S5 rotation detector FS_D0Q1 0.0 0.0 1.0 24.0035125 34.876875 0.0 detector_sensor . .
FS_D0Q1S5A0 rotation detector FS_D0Q1S5 0 0 1 -10.835 0.0 0.0 detector_asic 180.02434 FS_D0Q1S5
AXIS_D0Q1S5A0_F translation detector FS_D0Q1S5A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S5A0_S translation detector AXIS_D0Q1S5A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S5A1 rotation detector FS_D0Q1S5 0 0 1 10.835 0.0 0.0 detector_asic 180.02434 FS_D0Q1S5
AXIS_D0Q1S5A1_F translation detector FS_D0Q1S5A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S5A1_S translation detector AXIS_D0Q1S5A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S6 rotation detector FS_D0Q1 0.0 0.0 1.0 33.2523125 -23.321925 0.0 detector_sensor . .
FS_D0Q1S6A0 rotation detector FS_D0Q1S6 0 0 1 -10.835 0.0 0.0 detector_asic 270.08027 FS_D0Q1S6
AXIS_D0Q1S6A0_F translation detector FS_D0Q1S6A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S6A0_S translation detector AXIS_D0Q1S6A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S6A1 rotation detector FS_D0Q1S6 0 0 1 10.835 0.0 0.0 detector_asic 270.08027 FS_D0Q1S6
AXIS_D0Q1S6A1_F translation detector FS_D0Q1S6A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S6A1_S translation detector AXIS_D0Q1S6A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S7 rotation detector FS_D0Q1 0.0 0.0 1.0 9.9785125 -23.358225 0.0 detector_sensor . .
FS_D0Q1S7A0 rotation detector FS_D0Q1S7 0 0 1 -10.835 0.0 0.0 detector_asic 270.15067 FS_D0Q1S7
AXIS_D0Q1S7A0_F translation detector FS_D0Q1S7A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S7A0_S translation detector AXIS_D0Q1S7A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q1S7A1 rotation detector FS_D0Q1S7 0 0 1 10.835 0.0 0.0 detector_asic 270.15067 FS_D0Q1S7
AXIS_D0Q1S7A1_F translation detector FS_D0Q1S7A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q1S7A1_S translation detector AXIS_D0Q1S7A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2 rotation detector AXIS_D0_R 0 0 1 49.596146875 -41.351371875 0.0 detector_quadrant . .
FS_D0Q2S0 rotation detector FS_D0Q2 -0.0 -0.0 -1.0 -11.3150125 23.1242 0.0 detector_sensor . .
FS_D0Q2S0A0 rotation detector FS_D0Q2S0 0 0 1 -10.835 0.0 0.0 detector_asic 90.04803 FS_D0Q2S0
AXIS_D0Q2S0A0_F translation detector FS_D0Q2S0A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S0A0_S translation detector AXIS_D0Q2S0A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S0A1 rotation detector FS_D0Q2S0 0 0 1 10.835 0.0 0.0 detector_asic 90.04803 FS_D0Q2S0
AXIS_D0Q2S0A1_F translation detector FS_D0Q2S0A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S0A1_S translation detector AXIS_D0Q2S0A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S1 rotation detector FS_D0Q2 -0.0 -0.0 -1.0 -34.6999125 23.155 0.0 detector_sensor . .
FS_D0Q2S1A0 rotation detector FS_D0Q2S1 0 0 1 -10.835 0.0 0.0 detector_asic 90.00592 FS_D0Q2S1
AXIS_D0Q2S1A0_F translation detector FS_D0Q2S1A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S1A0_S translation detector AXIS_D0Q2S1A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S1A1 rotation detector FS_D0Q2S1 0 0 1 10.835 0.0 0.0 detector_asic 90.00592 FS_D0Q2S1
AXIS_D0Q2S1A1_F translation detector FS_D0Q2S1A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S1A1_S translation detector AXIS_D0Q2S1A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S2 rotation detector FS_D0Q2 0.0 0.0 1.0 23.4746875 10.7811 0.0 detector_sensor . .
FS_D0Q2S2A0 rotation detector FS_D0Q2S2 0 0 1 -10.835 0.0 0.0 detector_asic 180.11318 FS_D0Q2S2
AXIS_D0Q2S2A0_F translation detector FS_D0Q2S2A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S2A0_S translation detector AXIS_D0Q2S2A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S2A1 rotation detector FS_D0Q2S2 0 0 1 10.835 0.0 0.0 detector_asic 180.11318 FS_D0Q2S2
AXIS_D0Q2S2A1_F translation detector FS_D0Q2S2A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S2A1_S translation detector AXIS_D0Q2S2A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S3 rotation detector FS_D0Q2 0.0 0.0 1.0 23.6220875 34.2221 0.0 detector_sensor . .
FS_D0Q2S3A0 rotation detector FS_D0Q2S3 0 0 1 -10.835 0.0 0.0 detector_asic 179.92104 FS_D0Q2S3
AXIS_D0Q2S3A0_F translation detector FS_D0Q2S3A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S3A0_S translation detector AXIS_D0Q2S3A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S3A1 rotation detector FS_D0Q2S3 0 0 1 10.835 0.0 0.0 detector_asic 179.92104 FS_D0Q2S3
AXIS_D0Q2S3A1_F translation detector FS_D0Q2S3A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S3A1_S translation detector AXIS_D0Q2S3A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S4 rotation detector FS_D0Q2 0.0 0.0 1.0 11.1953875 -23.9954 0.0 detector_sensor . .
FS_D0Q2S4A0 rotation detector FS_D0Q2S4 0 0 1 -10.835 0.0 0.0 detector_asic 89.63875 FS_D0Q2S4
AXIS_D0Q2S4A0_F translation detector FS_D0Q2S4A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S4A0_S translation detector AXIS_D0Q2S4A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S4A1 rotation detector FS_D0Q2S4 0 0 1 10.835 0.0 0.0 detector_asic 89.63875 FS_D0Q2S4
AXIS_D0Q2S4A1_F translation detector FS_D0Q2S4A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S4A1_S translation detector AXIS_D0Q2S4A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S5 rotation detector FS_D0Q2 0.0 0.0 1.0 34.5494875 -24.1901 0.0 detector_sensor . .
FS_D0Q2S5A0 rotation detector FS_D0Q2S5 0 0 1 -10.835 0.0 0.0 detector_asic 89.68154 FS_D0Q2S5
AXIS_D0Q2S5A0_F translation detector FS_D0Q2S5A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S5A0_S translation detector AXIS_D0Q2S5A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S5A1 rotation detector FS_D0Q2S5 0 0 1 10.835 0.0 0.0 detector_asic 89.68154 FS_D0Q2S5
AXIS_D0Q2S5A1_F translation detector FS_D0Q2S5A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S5A1_S translation detector AXIS_D0Q2S5A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S6 rotation detector FS_D0Q2 0.0 0.0 1.0 -23.4854125 -33.2552 0.0 detector_sensor . .
FS_D0Q2S6A0 rotation detector FS_D0Q2S6 0 0 1 -10.835 0.0 0.0 detector_asic 179.83473 FS_D0Q2S6
AXIS_D0Q2S6A0_F translation detector FS_D0Q2S6A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S6A0_S translation detector AXIS_D0Q2S6A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S6A1 rotation detector FS_D0Q2S6 0 0 1 10.835 0.0 0.0 detector_asic 179.83473 FS_D0Q2S6
AXIS_D0Q2S6A1_F translation detector FS_D0Q2S6A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S6A1_S translation detector AXIS_D0Q2S6A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S7 rotation detector FS_D0Q2 0.0 0.0 1.0 -23.3413125 -9.8417 0.0 detector_sensor . .
FS_D0Q2S7A0 rotation detector FS_D0Q2S7 0 0 1 -10.835 0.0 0.0 detector_asic 180.092 FS_D0Q2S7
AXIS_D0Q2S7A0_F translation detector FS_D0Q2S7A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S7A0_S translation detector AXIS_D0Q2S7A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q2S7A1 rotation detector FS_D0Q2S7 0 0 1 10.835 0.0 0.0 detector_asic 180.092 FS_D0Q2S7
AXIS_D0Q2S7A1_F translation detector FS_D0Q2S7A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q2S7A1_S translation detector AXIS_D0Q2S7A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3 rotation detector AXIS_D0_R 0 0 1 -41.247903125 -50.441634375 0.0 detector_quadrant . .
FS_D0Q3S0 rotation detector FS_D0Q3 0.0 0.0 1.0 23.1056375 11.6367625 0.0 detector_sensor . .
FS_D0Q3S0A0 rotation detector FS_D0Q3S0 0 0 1 -10.835 0.0 0.0 detector_asic 180.12436 FS_D0Q3S0
AXIS_D0Q3S0A0_F translation detector FS_D0Q3S0A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S0A0_S translation detector AXIS_D0Q3S0A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S0A1 rotation detector FS_D0Q3S0 0 0 1 10.835 0.0 0.0 detector_asic 180.12436 FS_D0Q3S0
AXIS_D0Q3S0A1_F translation detector FS_D0Q3S0A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S0A1_S translation detector AXIS_D0Q3S0A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S1 rotation detector FS_D0Q3 0.0 0.0 1.0 23.1298375 34.9864625 0.0 detector_sensor . .
FS_D0Q3S1A0 rotation detector FS_D0Q3S1 0 0 1 -10.835 0.0 0.0 detector_asic 180.00263 FS_D0Q3S1
AXIS_D0Q3S1A0_F translation detector FS_D0Q3S1A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S1A0_S translation detector AXIS_D0Q3S1A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S1A1 rotation detector FS_D0Q3S1 0 0 1 10.835 0.0 0.0 detector_asic 180.00263 FS_D0Q3S1
AXIS_D0Q3S1A1_F translation detector FS_D0Q3S1A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S1A1_S translation detector AXIS_D0Q3S1A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S2 rotation detector FS_D0Q3 -0.0 -0.0 -1.0 10.9572375 -23.5830375 0.0 detector_sensor . .
FS_D0Q3S2A0 rotation detector FS_D0Q3S2 0 0 1 -10.835 0.0 0.0 detector_asic 269.55191 FS_D0Q3S2
AXIS_D0Q3S2A0_F translation detector FS_D0Q3S2A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S2A0_S translation detector AXIS_D0Q3S2A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S2A1 rotation detector FS_D0Q3S2 0 0 1 10.835 0.0 0.0 detector_asic 269.55191 FS_D0Q3S2
AXIS_D0Q3S2A1_F translation detector FS_D0Q3S2A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S2A1_S translation detector AXIS_D0Q3S2A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S3 rotation detector FS_D0Q3 -0.0 -0.0 -1.0 34.4180375 -23.4818375 0.0 detector_sensor . .
FS_D0Q3S3A0 rotation detector FS_D0Q3S3 0 0 1 -10.835 0.0 0.0 detector_asic 269.74206 FS_D0Q3S3
AXIS_D0Q3S3A0_F translation detector FS_D0Q3S3A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S3A0_S translation detector AXIS_D0Q3S3A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S3A1 rotation detector FS_D0Q3S3 0 0 1 10.835 0.0 0.0 detector_asic 269.74206 FS_D0Q3S3
AXIS_D0Q3S3A1_F translation detector FS_D0Q3S3A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S3A1_S translation detector AXIS_D0Q3S3A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S4 rotation detector FS_D0Q3 0.0 0.0 1.0 -24.1283625 -11.5336375 0.0 detector_sensor . .
FS_D0Q3S4A0 rotation detector FS_D0Q3S4 0 0 1 -10.835 0.0 0.0 detector_asic 359.81971 FS_D0Q3S4
AXIS_D0Q3S4A0_F translation detector FS_D0Q3S4A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S4A0_S translation detector AXIS_D0Q3S4A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S4A1 rotation detector FS_D0Q3S4 0 0 1 10.835 0.0 0.0 detector_asic 359.81971 FS_D0Q3S4
AXIS_D0Q3S4A1_F translation detector FS_D0Q3S4A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S4A1_S translation detector AXIS_D0Q3S4A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S5 rotation detector FS_D0Q3 0.0 0.0 1.0 -24.1701625 -34.9548375 0.0 detector_sensor . .
FS_D0Q3S5A0 rotation detector FS_D0Q3S5 0 0 1 -10.835 0.0 0.0 detector_asic 359.99883 FS_D0Q3S5
AXIS_D0Q3S5A0_F translation detector FS_D0Q3S5A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S5A0_S translation detector AXIS_D0Q3S5A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S5A1 rotation detector FS_D0Q3S5 0 0 1 10.835 0.0 0.0 detector_asic 359.99883 FS_D0Q3S5
AXIS_D0Q3S5A1_F translation detector FS_D0Q3S5A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S5A1_S translation detector AXIS_D0Q3S5A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S6 rotation detector FS_D0Q3 -0.0 -0.0 -1.0 -33.3089625 23.4474625 0.0 detector_sensor . .
FS_D0Q3S6A0 rotation detector FS_D0Q3S6 0 0 1 -10.835 0.0 0.0 detector_asic 269.67299 FS_D0Q3S6
AXIS_D0Q3S6A0_F translation detector FS_D0Q3S6A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S6A0_S translation detector AXIS_D0Q3S6A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S6A1 rotation detector FS_D0Q3S6 0 0 1 10.835 0.0 0.0 detector_asic 269.67299 FS_D0Q3S6
AXIS_D0Q3S6A1_F translation detector FS_D0Q3S6A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S6A1_S translation detector AXIS_D0Q3S6A1_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S7 rotation detector FS_D0Q3 -0.0 -0.0 -1.0 -10.0032625 23.4826625 0.0 detector_sensor . .
FS_D0Q3S7A0 rotation detector FS_D0Q3S7 0 0 1 -10.835 0.0 0.0 detector_asic 269.67561 FS_D0Q3S7
AXIS_D0Q3S7A0_F translation detector FS_D0Q3S7A0 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S7A0_S translation detector AXIS_D0Q3S7A0_F 0 -1 0 0 0 0.0 detector_asic . .
FS_D0Q3S7A1 rotation detector FS_D0Q3S7 0 0 1 10.835 0.0 0.0 detector_asic 269.67561 FS_D0Q3S7
AXIS_D0Q3S7A1_F translation detector FS_D0Q3S7A1 1 0 0 -10.615000 10.120000 0.0 detector_asic . .
AXIS_D0Q3S7A1_S translation detector AXIS_D0Q3S7A1_F 0 -1 0 0 0 0.0 detector_asic . .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 6 -
This example show an excerpt from the axis specification of an FEL detector
provided by N. Sauter and A. Brewster, using _axis.rotation_axis and
_axis.rotation to organize the positional dependencies. The approach
in Example 5 is now preferred.
The detector is divided into 4 quadrants, each quadrant contains 8 sensors
and each sensor contains 2 ASICs. We want to be able to refine the
placement of each of these elements, so we maintain the set of vectors
that places them.
To do this, the first vector of importance is an initial placement axis
that moves from the origin along the Z axis a distance equal to the
detector distance. This is the origin for the rest of the axes and is
called AXIS_D0_ORIGIN.
Each subsequent movement involves a frame shift. This is done by using
two imageCIF axes: a rotation axis and a translation axis. The rotation
axis is listed first, and includes no offset or angle. The actual frame
shift is done by using a translation axis. An offset is used first in
the parent's frame, and then an angle is listed to rotate around the
rotation axis.
Example, sensor five of quadrant 2. First a rotation axis is listed:
AXIS_D0Q2S5_ROT rotation detector AXIS_D0Q2 0.0 0.0 1.0 0 0 0 . .
This defines a rotation axis around the z-axis in the frame of quadrant 2.
Next a translation axis is listed:
AXIS_D0Q2S5 translation detector
AXIS_D0Q2 . . . 34.5494875 -24.1901 0.0 89.68154 AXIS_D0Q2S5_ROT
Here, in the frame of quadrant 2, we shift X by 34 and Y by -24
millimeters, then rotate 89 degrees around the axis named AXIS_D0Q2S5_ROT.
And so forth.
;
;
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
CSPAD_FRONT AXIS_DETECTOR_X
CSPAD_FRONT AXIS_DETECTOR_Y
CSPAD_FRONT AXIS_DETECTOR_Z
CSPAD_FRONT AXIS_DETECTOR_PITCH
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELE_D0Q0S0A0 CSPAD_FRONT
ELE_D0Q0S0A1 CSPAD_FRONT
ELE_D0Q0S1A0 CSPAD_FRONT
ELE_D0Q0S1A1 CSPAD_FRONT
ELE_D0Q0S2A0 CSPAD_FRONT
ELE_D0Q0S2A1 CSPAD_FRONT
ELE_D0Q0S3A0 CSPAD_FRONT
ELE_D0Q0S3A1 CSPAD_FRONT
ELE_D0Q0S4A0 CSPAD_FRONT
ELE_D0Q0S4A1 CSPAD_FRONT
ELE_D0Q0S5A0 CSPAD_FRONT
ELE_D0Q0S5A1 CSPAD_FRONT
ELE_D0Q0S6A0 CSPAD_FRONT
ELE_D0Q0S6A1 CSPAD_FRONT
ELE_D0Q0S7A0 CSPAD_FRONT
ELE_D0Q0S7A1 CSPAD_FRONT
ELE_D0Q1S0A0 CSPAD_FRONT
ELE_D0Q1S0A1 CSPAD_FRONT
ELE_D0Q1S1A0 CSPAD_FRONT
ELE_D0Q1S1A1 CSPAD_FRONT
ELE_D0Q1S2A0 CSPAD_FRONT
ELE_D0Q1S2A1 CSPAD_FRONT
ELE_D0Q1S3A0 CSPAD_FRONT
ELE_D0Q1S3A1 CSPAD_FRONT
ELE_D0Q1S4A0 CSPAD_FRONT
ELE_D0Q1S4A1 CSPAD_FRONT
ELE_D0Q1S5A0 CSPAD_FRONT
ELE_D0Q1S5A1 CSPAD_FRONT
ELE_D0Q1S6A0 CSPAD_FRONT
ELE_D0Q1S6A1 CSPAD_FRONT
ELE_D0Q1S7A0 CSPAD_FRONT
ELE_D0Q1S7A1 CSPAD_FRONT
ELE_D0Q2S0A0 CSPAD_FRONT
ELE_D0Q2S0A1 CSPAD_FRONT
ELE_D0Q2S1A0 CSPAD_FRONT
ELE_D0Q2S1A1 CSPAD_FRONT
ELE_D0Q2S2A0 CSPAD_FRONT
ELE_D0Q2S2A1 CSPAD_FRONT
ELE_D0Q2S3A0 CSPAD_FRONT
ELE_D0Q2S3A1 CSPAD_FRONT
ELE_D0Q2S4A0 CSPAD_FRONT
ELE_D0Q2S4A1 CSPAD_FRONT
ELE_D0Q2S5A0 CSPAD_FRONT
ELE_D0Q2S5A1 CSPAD_FRONT
ELE_D0Q2S6A0 CSPAD_FRONT
ELE_D0Q2S6A1 CSPAD_FRONT
ELE_D0Q2S7A0 CSPAD_FRONT
ELE_D0Q2S7A1 CSPAD_FRONT
ELE_D0Q3S0A0 CSPAD_FRONT
ELE_D0Q3S0A1 CSPAD_FRONT
ELE_D0Q3S1A0 CSPAD_FRONT
ELE_D0Q3S1A1 CSPAD_FRONT
ELE_D0Q3S2A0 CSPAD_FRONT
ELE_D0Q3S2A1 CSPAD_FRONT
ELE_D0Q3S3A0 CSPAD_FRONT
ELE_D0Q3S3A1 CSPAD_FRONT
ELE_D0Q3S4A0 CSPAD_FRONT
ELE_D0Q3S4A1 CSPAD_FRONT
ELE_D0Q3S5A0 CSPAD_FRONT
ELE_D0Q3S5A1 CSPAD_FRONT
ELE_D0Q3S6A0 CSPAD_FRONT
ELE_D0Q3S6A1 CSPAD_FRONT
ELE_D0Q3S7A0 CSPAD_FRONT
ELE_D0Q3S7A1 CSPAD_FRONT
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]
_axis.rotation
_axis.rotation_axis
AXIS_SOURCE general source . 0 0 1 . . . . .
AXIS_GRAVITY general gravity . 0 -1 0 . . . . .
AXIS_DETECTOR_Z translation detector
. 0 0 1 0 0 0 . .
AXIS_DETECTOR_Y translation detector
AXIS_DETECTOR_Z 0 1 0 0 0 0 . .
AXIS_DETECTOR_X translation detector
AXIS_DETECTOR_Y 1 0 0 0 0 0 . .
AXIS_DETECTOR_PITCH rotation detector
AXIS_DETECTOR_X 0 1 0 0 0 0 . .
AXIS_DETECTOR_ROT rotation detector
AXIS_DETECTOR_PITCH 0 0 1 0 0 0 . .
AXIS_D0_ORIGIN translation detector
AXIS_DETECTOR_PITCH 0 0 1 0 0 171.0104 . .
AXIS_D0_ROT rotation detector
AXIS_D0_ORIGIN 0.0 0.0 0.0 0 0 0 . .
AXIS_D0 translation detector
AXIS_D0_ORIGIN . . . 0.0 0.0 0.0 0.0 AXIS_D0_ROT
AXIS_D0Q0_ROT rotation detector
AXIS_D0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0 translation detector
AXIS_D0 . . . -49.860765625 41.643353125 0.0
0.0 AXIS_D0Q0_ROT
AXIS_D0Q0S0_ROT rotation detector
AXIS_D0Q0 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q0S0 translation detector
AXIS_D0Q0 . . . 11.3696 -23.189925 0.0
89.66181 AXIS_D0Q0S0_ROT
AXIS_D0Q0S0A0_ROT rotation detector
AXIS_D0Q0S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S0A0 translation detector
AXIS_D0Q0S0 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S0A0_ROT
AXIS_D0Q0S0A0_F translation detector
AXIS_D0Q0S0A0 1 0 0 0 0 0 . .
AXIS_D0Q0S0A0_S translation detector
AXIS_D0Q0S0A0 0 1 0 0 0 0 . .
AXIS_D0Q0S0A1_ROT rotation detector
AXIS_D0Q0S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S0A1 translation detector
AXIS_D0Q0S0 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S0A1_ROT
AXIS_D0Q0S0A1_F translation detector
AXIS_D0Q0S0A1 1 0 0 0 0 0 . .
AXIS_D0Q0S0A1_S translation detector
AXIS_D0Q0S0A1 0 1 0 0 0 0 . .
AXIS_D0Q0S1_ROT rotation detector
AXIS_D0Q0 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q0S1 translation detector
AXIS_D0Q0 . . . 34.815 -23.309825 0.0
90.00132 AXIS_D0Q0S1_ROT
AXIS_D0Q0S1A0_ROT rotation detector
AXIS_D0Q0S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S1A0 translation detector
AXIS_D0Q0S1 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S1A0_ROT
AXIS_D0Q0S1A0_F translation detector
AXIS_D0Q0S1A0 1 0 0 0 0 0 . .
AXIS_D0Q0S1A0_S translation detector
AXIS_D0Q0S1A0 0 1 0 0 0 0 . .
AXIS_D0Q0S1A1_ROT rotation detector
AXIS_D0Q0S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S1A1 translation detector
AXIS_D0Q0S1 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S1A1_ROT
AXIS_D0Q0S1A1_F translation detector
AXIS_D0Q0S1A1 1 0 0 0 0 0 . .
AXIS_D0Q0S1A1_S translation detector
AXIS_D0Q0S1A1 0 1 0 0 0 0 . .
AXIS_D0Q0S2_ROT rotation detector
AXIS_D0Q0 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q0S2 translation detector
AXIS_D0Q0 . . . -23.5389 -10.921625 0.0
359.68548 AXIS_D0Q0S2_ROT
AXIS_D0Q0S2A0_ROT rotation detector
AXIS_D0Q0S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S2A0 translation detector
AXIS_D0Q0S2 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S2A0_ROT
AXIS_D0Q0S2A0_F translation detector
AXIS_D0Q0S2A0 1 0 0 0 0 0 . .
AXIS_D0Q0S2A0_S translation detector
AXIS_D0Q0S2A0 0 1 0 0 0 0 . .
AXIS_D0Q0S2A1_ROT rotation detector
AXIS_D0Q0S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S2A1 translation detector
AXIS_D0Q0S2 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S2A1_ROT
AXIS_D0Q0S2A1_F translation detector
AXIS_D0Q0S2A1 1 0 0 0 0 0 . .
AXIS_D0Q0S2A1_S translation detector
AXIS_D0Q0S2A1 0 1 0 0 0 0 . .
AXIS_D0Q0S3_ROT rotation detector
AXIS_D0Q0 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q0S3 translation detector
AXIS_D0Q0 . . . -23.5499 -34.181125 0.0
359.96513 AXIS_D0Q0S3_ROT
AXIS_D0Q0S3A0_ROT rotation detector
AXIS_D0Q0S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S3A0 translation detector
AXIS_D0Q0S3 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S3A0_ROT
AXIS_D0Q0S3A0_F translation detector
AXIS_D0Q0S3A0 1 0 0 0 0 0 . .
AXIS_D0Q0S3A0_S translation detector
AXIS_D0Q0S3A0 0 1 0 0 0 0 . .
AXIS_D0Q0S3A1_ROT rotation detector
AXIS_D0Q0S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S3A1 translation detector
AXIS_D0Q0S3 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S3A1_ROT
AXIS_D0Q0S3A1_F translation detector
AXIS_D0Q0S3A1 1 0 0 0 0 0 . .
AXIS_D0Q0S3A1_S translation detector
AXIS_D0Q0S3A1 0 1 0 0 0 0 . .
AXIS_D0Q0S4_ROT rotation detector
AXIS_D0Q0 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q0S4 translation detector
AXIS_D0Q0 . . . -11.2651 24.282775 0.0
270.14738 AXIS_D0Q0S4_ROT
AXIS_D0Q0S4A0_ROT rotation detector
AXIS_D0Q0S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S4A0 translation detector
AXIS_D0Q0S4 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S4A0_ROT
AXIS_D0Q0S4A0_F translation detector
AXIS_D0Q0S4A0 1 0 0 0 0 0 . .
AXIS_D0Q0S4A0_S translation detector
AXIS_D0Q0S4A0 0 1 0 0 0 0 . .
AXIS_D0Q0S4A1_ROT rotation detector
AXIS_D0Q0S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S4A1 translation detector
AXIS_D0Q0S4 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S4A1_ROT
AXIS_D0Q0S4A1_F translation detector
AXIS_D0Q0S4A1 1 0 0 0 0 0 . .
AXIS_D0Q0S4A1_S translation detector
AXIS_D0Q0S4A1 0 1 0 0 0 0 . .
AXIS_D0Q0S5_ROT rotation detector
AXIS_D0Q0 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q0S5 translation detector
AXIS_D0Q0 . . . -34.7336 24.169475 0.0
270.07896 AXIS_D0Q0S5_ROT
AXIS_D0Q0S5A0_ROT rotation detector
AXIS_D0Q0S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S5A0 translation detector
AXIS_D0Q0S5 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S5A0_ROT
AXIS_D0Q0S5A0_F translation detector
AXIS_D0Q0S5A0 1 0 0 0 0 0 . .
AXIS_D0Q0S5A0_S translation detector
AXIS_D0Q0S5A0 0 1 0 0 0 0 . .
AXIS_D0Q0S5A1_ROT rotation detector
AXIS_D0Q0S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S5A1 translation detector
AXIS_D0Q0S5 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S5A1_ROT
AXIS_D0Q0S5A1_F translation detector
AXIS_D0Q0S5A1 1 0 0 0 0 0 . .
AXIS_D0Q0S5A1_S translation detector
AXIS_D0Q0S5A1 0 1 0 0 0 0 . .
AXIS_D0Q0S6_ROT rotation detector
AXIS_D0Q0 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q0S6 translation detector
AXIS_D0Q0 . . . 23.5488 33.320375 0.0
359.78222 AXIS_D0Q0S6_ROT
AXIS_D0Q0S6A0_ROT rotation detector
AXIS_D0Q0S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S6A0 translation detector
AXIS_D0Q0S6 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S6A0_ROT
AXIS_D0Q0S6A0_F translation detector
AXIS_D0Q0S6A0 1 0 0 0 0 0 . .
AXIS_D0Q0S6A0_S translation detector
AXIS_D0Q0S6A0 0 1 0 0 0 0 . .
AXIS_D0Q0S6A1_ROT rotation detector
AXIS_D0Q0S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S6A1 translation detector
AXIS_D0Q0S6 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S6A1_ROT
AXIS_D0Q0S6A1_F translation detector
AXIS_D0Q0S6A1 1 0 0 0 0 0 . .
AXIS_D0Q0S6A1_S translation detector
AXIS_D0Q0S6A1 0 1 0 0 0 0 . .
AXIS_D0Q0S7_ROT rotation detector
AXIS_D0Q0 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q0S7 translation detector
AXIS_D0Q0 . . . 23.3541 9.829875 0.0
359.89604 AXIS_D0Q0S7_ROT
AXIS_D0Q0S7A0_ROT rotation detector
AXIS_D0Q0S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S7A0 translation detector
AXIS_D0Q0S7 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q0S7A0_ROT
AXIS_D0Q0S7A0_F translation detector
AXIS_D0Q0S7A0 1 0 0 0 0 0 . .
AXIS_D0Q0S7A0_S translation detector
AXIS_D0Q0S7A0 0 1 0 0 0 0 . .
AXIS_D0Q0S7A1_ROT rotation detector
AXIS_D0Q0S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q0S7A1 translation detector
AXIS_D0Q0S7 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q0S7A1_ROT
AXIS_D0Q0S7A1_F translation detector
AXIS_D0Q0S7A1 1 0 0 0 0 0 . .
AXIS_D0Q0S7A1_S translation detector
AXIS_D0Q0S7A1 0 1 0 0 0 0 . .
AXIS_D0Q1_ROT rotation detector
AXIS_D0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1 translation detector
AXIS_D0 . . . 41.512521875 50.149653125 0.0
0.0 AXIS_D0Q1_ROT
AXIS_D0Q1S0_ROT rotation detector
AXIS_D0Q1 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q1S0 translation detector
AXIS_D0Q1 . . . -23.1589875 -11.451825 0.0
0.27238 AXIS_D0Q1S0_ROT
AXIS_D0Q1S0A0_ROT rotation detector
AXIS_D0Q1S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S0A0 translation detector
AXIS_D0Q1S0 . . . -10.835 0.0 0.0
0.0 AXIS_D0Q1S0A0_ROT
AXIS_D0Q1S0A0_F translation detector
AXIS_D0Q1S0A0 1 0 0 0 0 0 . .
AXIS_D0Q1S0A0_S translation detector
AXIS_D0Q1S0A0 0 1 0 0 0 0 . .
AXIS_D0Q1S0A1_ROT rotation detector
AXIS_D0Q1S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S0A1 translation detector
AXIS_D0Q1S0 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S0A1_ROT
AXIS_D0Q1S0A1_F translation detector
AXIS_D0Q1S0A1 1 0 0 0 0 0 . .
AXIS_D0Q1S0A1_S translation detector
AXIS_D0Q1S0A1 0 1 0 0 0 0 . .
AXIS_D0Q1S1_ROT rotation detector
AXIS_D0Q1 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q1S1 translation detector
AXIS_D0Q1 . . . -23.2073875 -34.782825 0.0
0.00525999986641 AXIS_D0Q1S1_ROT
AXIS_D0Q1S1A0_ROT rotation detector
AXIS_D0Q1S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S1A0 translation detector
AXIS_D0Q1S1 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q1S1A0_ROT
AXIS_D0Q1S1A0_F translation detector
AXIS_D0Q1S1A0 1 0 0 0 0 0 . .
AXIS_D0Q1S1A0_S translation detector
AXIS_D0Q1S1A0 0 1 0 0 0 0 . .
AXIS_D0Q1S1A1_ROT rotation detector
AXIS_D0Q1S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S1A1 translation detector
AXIS_D0Q1S1 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S1A1_ROT
AXIS_D0Q1S1A1_F translation detector
AXIS_D0Q1S1A1 1 0 0 0 0 0 . .
AXIS_D0Q1S1A1_S translation detector
AXIS_D0Q1S1A1 0 1 0 0 0 0 . .
AXIS_D0Q1S2_ROT rotation detector
AXIS_D0Q1 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q1S2 translation detector
AXIS_D0Q1 . . . -10.7311875 23.286175 0.0
270.02545 AXIS_D0Q1S2_ROT
AXIS_D0Q1S2A0_ROT rotation detector
AXIS_D0Q1S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S2A0 translation detector
AXIS_D0Q1S2 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q1S2A0_ROT
AXIS_D0Q1S2A0_F translation detector
AXIS_D0Q1S2A0 1 0 0 0 0 0 . .
AXIS_D0Q1S2A0_S translation detector
AXIS_D0Q1S2A0 0 1 0 0 0 0 . .
AXIS_D0Q1S2A1_ROT rotation detector
AXIS_D0Q1S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S2A1 translation detector
AXIS_D0Q1S2 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S2A1_ROT
AXIS_D0Q1S2A1_F translation detector
AXIS_D0Q1S2A1 1 0 0 0 0 0 . .
AXIS_D0Q1S2A1_S translation detector
AXIS_D0Q1S2A1 0 1 0 0 0 0 . .
AXIS_D0Q1S3_ROT rotation detector
AXIS_D0Q1 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q1S3 translation detector
AXIS_D0Q1 . . . -34.1402875 23.344475 0.0
270.03066 AXIS_D0Q1S3_ROT
AXIS_D0Q1S3A0_ROT rotation detector
AXIS_D0Q1S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S3A0 translation detector
AXIS_D0Q1S3 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q1S3A0_ROT
AXIS_D0Q1S3A0_F translation detector
AXIS_D0Q1S3A0 1 0 0 0 0 0 . .
AXIS_D0Q1S3A0_S translation detector
AXIS_D0Q1S3A0 0 1 0 0 0 0 . .
AXIS_D0Q1S3A1_ROT rotation detector
AXIS_D0Q1S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S3A1 translation detector
AXIS_D0Q1S3 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S3A1_ROT
AXIS_D0Q1S3A1_F translation detector
AXIS_D0Q1S3A1 1 0 0 0 0 0 . .
AXIS_D0Q1S3A1_S translation detector
AXIS_D0Q1S3A1 0 1 0 0 0 0 . .
AXIS_D0Q1S4_ROT rotation detector
AXIS_D0Q1 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q1S4 translation detector
AXIS_D0Q1 . . . 24.0035125 11.407275 0.0
179.96381 AXIS_D0Q1S4_ROT
AXIS_D0Q1S4A0_ROT rotation detector
AXIS_D0Q1S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S4A0 translation detector
AXIS_D0Q1S4 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q1S4A0_ROT
AXIS_D0Q1S4A0_F translation detector
AXIS_D0Q1S4A0 1 0 0 0 0 0 . .
AXIS_D0Q1S4A0_S translation detector
AXIS_D0Q1S4A0 0 1 0 0 0 0 . .
AXIS_D0Q1S4A1_ROT rotation detector
AXIS_D0Q1S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S4A1 translation detector
AXIS_D0Q1S4 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S4A1_ROT
AXIS_D0Q1S4A1_F translation detector
AXIS_D0Q1S4A1 1 0 0 0 0 0 . .
AXIS_D0Q1S4A1_S translation detector
AXIS_D0Q1S4A1 0 1 0 0 0 0 . .
AXIS_D0Q1S5_ROT rotation detector
AXIS_D0Q1 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q1S5 translation detector
AXIS_D0Q1 . . . 24.0035125 34.876875 0.0
180.02434 AXIS_D0Q1S5_ROT
AXIS_D0Q1S5A0_ROT rotation detector
AXIS_D0Q1S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S5A0 translation detector
AXIS_D0Q1S5 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q1S5A0_ROT
AXIS_D0Q1S5A0_F translation detector
AXIS_D0Q1S5A0 1 0 0 0 0 0 . .
AXIS_D0Q1S5A0_S translation detector
AXIS_D0Q1S5A0 0 1 0 0 0 0 . .
AXIS_D0Q1S5A1_ROT rotation detector
AXIS_D0Q1S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S5A1 translation detector
AXIS_D0Q1S5 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S5A1_ROT
AXIS_D0Q1S5A1_F translation detector
AXIS_D0Q1S5A1 1 0 0 0 0 0 . .
AXIS_D0Q1S5A1_S translation detector
AXIS_D0Q1S5A1 0 1 0 0 0 0 . .
AXIS_D0Q1S6_ROT rotation detector
AXIS_D0Q1 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q1S6 translation detector
AXIS_D0Q1 . . . 33.2523125 -23.321925 0.0
270.08027 AXIS_D0Q1S6_ROT
AXIS_D0Q1S6A0_ROT rotation detector
AXIS_D0Q1S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S6A0 translation detector
AXIS_D0Q1S6 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q1S6A0_ROT
AXIS_D0Q1S6A0_F translation detector
AXIS_D0Q1S6A0 1 0 0 0 0 0 . .
AXIS_D0Q1S6A0_S translation detector
AXIS_D0Q1S6A0 0 1 0 0 0 0 . .
AXIS_D0Q1S6A1_ROT rotation detector
AXIS_D0Q1S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S6A1 translation detector
AXIS_D0Q1S6 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S6A1_ROT
AXIS_D0Q1S6A1_F translation detector
AXIS_D0Q1S6A1 1 0 0 0 0 0 . .
AXIS_D0Q1S6A1_S translation detector
AXIS_D0Q1S6A1 0 1 0 0 0 0 . .
AXIS_D0Q1S7_ROT rotation detector
AXIS_D0Q1 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q1S7 translation detector
AXIS_D0Q1 . . . 9.9785125 -23.358225 0.0
270.15067 AXIS_D0Q1S7_ROT
AXIS_D0Q1S7A0_ROT rotation detector
AXIS_D0Q1S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S7A0 translation detector
AXIS_D0Q1S7 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q1S7A0_ROT
AXIS_D0Q1S7A0_F translation detector
AXIS_D0Q1S7A0 1 0 0 0 0 0 . .
AXIS_D0Q1S7A0_S translation detector
AXIS_D0Q1S7A0 0 1 0 0 0 0 . .
AXIS_D0Q1S7A1_ROT rotation detector
AXIS_D0Q1S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q1S7A1 translation detector
AXIS_D0Q1S7 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q1S7A1_ROT
AXIS_D0Q1S7A1_F translation detector
AXIS_D0Q1S7A1 1 0 0 0 0 0 . .
AXIS_D0Q1S7A1_S translation detector
AXIS_D0Q1S7A1 0 1 0 0 0 0 . .
AXIS_D0Q2_ROT rotation detector
AXIS_D0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2 translation detector
AXIS_D0 . . . 49.596146875 -41.351371875 0.0
0.0 AXIS_D0Q2_ROT
AXIS_D0Q2S0_ROT rotation detector
AXIS_D0Q2 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q2S0 translation detector
AXIS_D0Q2 . . . -11.3150125 23.1242 0.0
90.04803 AXIS_D0Q2S0_ROT
AXIS_D0Q2S0A0_ROT rotation detector
AXIS_D0Q2S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S0A0 translation detector
AXIS_D0Q2S0 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q2S0A0_ROT
AXIS_D0Q2S0A0_F translation detector
AXIS_D0Q2S0A0 1 0 0 0 0 0 . .
AXIS_D0Q2S0A0_S translation detector
AXIS_D0Q2S0A0 0 1 0 0 0 0 . .
AXIS_D0Q2S0A1_ROT rotation detector
AXIS_D0Q2S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S0A1 translation detector
AXIS_D0Q2S0 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q2S0A1_ROT
AXIS_D0Q2S0A1_F translation detector
AXIS_D0Q2S0A1 1 0 0 0 0 0 . .
AXIS_D0Q2S0A1_S translation detector
AXIS_D0Q2S0A1 0 1 0 0 0 0 . .
AXIS_D0Q2S1_ROT rotation detector
AXIS_D0Q2 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q2S1 translation detector
AXIS_D0Q2 . . . -34.6999125 23.155 0.0
90.00592 AXIS_D0Q2S1_ROT
AXIS_D0Q2S1A0_ROT rotation detector
AXIS_D0Q2S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S1A0 translation detector
AXIS_D0Q2S1 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q2S1A0_ROT
AXIS_D0Q2S1A0_F translation detector
AXIS_D0Q2S1A0 1 0 0 0 0 0 . .
AXIS_D0Q2S1A0_S translation detector
AXIS_D0Q2S1A0 0 1 0 0 0 0 . .
AXIS_D0Q2S1A1_ROT rotation detector
AXIS_D0Q2S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S1A1 translation detector
AXIS_D0Q2S1 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q2S1A1_ROT
AXIS_D0Q2S1A1_F translation detector
AXIS_D0Q2S1A1 1 0 0 0 0 0 . .
AXIS_D0Q2S1A1_S translation detector
AXIS_D0Q2S1A1 0 1 0 0 0 0 . .
AXIS_D0Q2S2_ROT rotation detector
AXIS_D0Q2 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q2S2 translation detector
AXIS_D0Q2 . . . 23.4746875 10.7811 0.0
180.11318 AXIS_D0Q2S2_ROT
AXIS_D0Q2S2A0_ROT rotation detector
AXIS_D0Q2S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S2A0 translation detector
AXIS_D0Q2S2 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q2S2A0_ROT
AXIS_D0Q2S2A0_F translation detector
AXIS_D0Q2S2A0 1 0 0 0 0 0 . .
AXIS_D0Q2S2A0_S translation detector
AXIS_D0Q2S2A0 0 1 0 0 0 0 . .
AXIS_D0Q2S2A1_ROT rotation detector
AXIS_D0Q2S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S2A1 translation detector
AXIS_D0Q2S2 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q2S2A1_ROT
AXIS_D0Q2S2A1_F translation detector
AXIS_D0Q2S2A1 1 0 0 0 0 0 . .
AXIS_D0Q2S2A1_S translation detector
AXIS_D0Q2S2A1 0 1 0 0 0 0 . .
AXIS_D0Q2S3_ROT rotation detector
AXIS_D0Q2 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q2S3 translation detector
AXIS_D0Q2 . . . 23.6220875 34.2221 0.0
179.92104 AXIS_D0Q2S3_ROT
AXIS_D0Q2S3A0_ROT rotation detector
AXIS_D0Q2S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S3A0 translation detector
AXIS_D0Q2S3 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q2S3A0_ROT
AXIS_D0Q2S3A0_F translation detector
AXIS_D0Q2S3A0 1 0 0 0 0 0 . .
AXIS_D0Q2S3A0_S translation detector
AXIS_D0Q2S3A0 0 1 0 0 0 0 . .
AXIS_D0Q2S3A1_ROT rotation detector
AXIS_D0Q2S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S3A1 translation detector
AXIS_D0Q2S3 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q2S3A1_ROT
AXIS_D0Q2S3A1_F translation detector
AXIS_D0Q2S3A1 1 0 0 0 0 0 . .
AXIS_D0Q2S3A1_S translation detector
AXIS_D0Q2S3A1 0 1 0 0 0 0 . .
AXIS_D0Q2S4_ROT rotation detector
AXIS_D0Q2 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q2S4 translation detector
AXIS_D0Q2 . . . 11.1953875 -23.9954 0.0
89.63875 AXIS_D0Q2S4_ROT
AXIS_D0Q2S4A0_ROT rotation detector
AXIS_D0Q2S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S4A0 translation detector
AXIS_D0Q2S4 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q2S4A0_ROT
AXIS_D0Q2S4A0_F translation detector
AXIS_D0Q2S4A0 1 0 0 0 0 0 . .
AXIS_D0Q2S4A0_S translation detector
AXIS_D0Q2S4A0 0 1 0 0 0 0 . .
AXIS_D0Q2S4A1_ROT rotation detector
AXIS_D0Q2S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S4A1 translation detector
AXIS_D0Q2S4 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q2S4A1_ROT
AXIS_D0Q2S4A1_F translation detector
AXIS_D0Q2S4A1 1 0 0 0 0 0 . .
AXIS_D0Q2S4A1_S translation detector
AXIS_D0Q2S4A1 0 1 0 0 0 0 . .
AXIS_D0Q2S5_ROT rotation detector
AXIS_D0Q2 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q2S5 translation detector
AXIS_D0Q2 . . . 34.5494875 -24.1901 0.0
89.68154 AXIS_D0Q2S5_ROT
AXIS_D0Q2S5A0_ROT rotation detector
AXIS_D0Q2S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S5A0 translation detector
AXIS_D0Q2S5 . . . -10.835 0.0 0.0
0.0 AXIS_D0Q2S5A0_ROT
AXIS_D0Q2S5A0_F translation detector
AXIS_D0Q2S5A0 1 0 0 0 0 0 . .
AXIS_D0Q2S5A0_S translation detector
AXIS_D0Q2S5A0 0 1 0 0 0 0 . .
AXIS_D0Q2S5A1_ROT rotation detector
AXIS_D0Q2S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S5A1 translation detector
AXIS_D0Q2S5 . . . 10.835 0.0 0.0
0.0 AXIS_D0Q2S5A1_ROT
AXIS_D0Q2S5A1_F translation detector
AXIS_D0Q2S5A1 1 0 0 0 0 0 . .
AXIS_D0Q2S5A1_S translation detector
AXIS_D0Q2S5A1 0 1 0 0 0 0 . .
AXIS_D0Q2S6_ROT rotation detector
AXIS_D0Q2 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q2S6 translation detector
AXIS_D0Q2 . . . -23.4854125 -33.2552 0.0
179.83473 AXIS_D0Q2S6_ROT
AXIS_D0Q2S6A0_ROT rotation detector
AXIS_D0Q2S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S6A0 translation detector
AXIS_D0Q2S6 . . . -10.835 0.0 0.0
0.0 AXIS_D0Q2S6A0_ROT
AXIS_D0Q2S6A0_F translation detector
AXIS_D0Q2S6A0 1 0 0 0 0 0 . .
AXIS_D0Q2S6A0_S translation detector
AXIS_D0Q2S6A0 0 1 0 0 0 0 . .
AXIS_D0Q2S6A1_ROT rotation detector
AXIS_D0Q2S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S6A1 translation detector
AXIS_D0Q2S6 . . . 10.835 0.0 0.0
0.0 AXIS_D0Q2S6A1_ROT
AXIS_D0Q2S6A1_F translation detector
AXIS_D0Q2S6A1 1 0 0 0 0 0 . .
AXIS_D0Q2S6A1_S translation detector
AXIS_D0Q2S6A1 0 1 0 0 0 0 . .
AXIS_D0Q2S7_ROT rotation detector
AXIS_D0Q2 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q2S7 translation detector
AXIS_D0Q2 . . . -23.3413125 -9.8417 0.0
180.092 AXIS_D0Q2S7_ROT
AXIS_D0Q2S7A0_ROT rotation detector
AXIS_D0Q2S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S7A0 translation detector
AXIS_D0Q2S7 . . . -10.835 0.0 0.0
0.0 AXIS_D0Q2S7A0_ROT
AXIS_D0Q2S7A0_F translation detector
AXIS_D0Q2S7A0 1 0 0 0 0 0 . .
AXIS_D0Q2S7A0_S translation detector
AXIS_D0Q2S7A0 0 1 0 0 0 0 . .
AXIS_D0Q2S7A1_ROT rotation detector
AXIS_D0Q2S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q2S7A1 translation detector
AXIS_D0Q2S7 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q2S7A1_ROT
AXIS_D0Q2S7A1_F translation detector
AXIS_D0Q2S7A1 1 0 0 0 0 0 . .
AXIS_D0Q2S7A1_S translation detector
AXIS_D0Q2S7A1 0 1 0 0 0 0 . .
AXIS_D0Q3_ROT rotation detector
AXIS_D0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3 translation detector
AXIS_D0 . . . -41.247903125 -50.441634375 0.0
0.0 AXIS_D0Q3_ROT
AXIS_D0Q3S0_ROT rotation detector
AXIS_D0Q3 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q3S0 translation detector
AXIS_D0Q3 . . . 23.1056375 11.6367625 0.0
180.12436 AXIS_D0Q3S0_ROT
AXIS_D0Q3S0A0_ROT rotation detector
AXIS_D0Q3S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S0A0 translation detector
AXIS_D0Q3S0 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S0A0_ROT
AXIS_D0Q3S0A0_F translation detector
AXIS_D0Q3S0A0 1 0 0 0 0 0 . .
AXIS_D0Q3S0A0_S translation detector
AXIS_D0Q3S0A0 0 1 0 0 0 0 . .
AXIS_D0Q3S0A1_ROT rotation detector
AXIS_D0Q3S0 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S0A1 translation detector
AXIS_D0Q3S0 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S0A1_ROT
AXIS_D0Q3S0A1_F translation detector
AXIS_D0Q3S0A1 1 0 0 0 0 0 . .
AXIS_D0Q3S0A1_S translation detector
AXIS_D0Q3S0A1 0 1 0 0 0 0 . .
AXIS_D0Q3S1_ROT rotation detector
AXIS_D0Q3 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q3S1 translation detector
AXIS_D0Q3 . . . 23.1298375 34.9864625 0.0
180.00263 AXIS_D0Q3S1_ROT
AXIS_D0Q3S1A0_ROT rotation detector
AXIS_D0Q3S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S1A0 translation detector
AXIS_D0Q3S1 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S1A0_ROT
AXIS_D0Q3S1A0_F translation detector
AXIS_D0Q3S1A0 1 0 0 0 0 0 . .
AXIS_D0Q3S1A0_S translation detector
AXIS_D0Q3S1A0 0 1 0 0 0 0 . .
AXIS_D0Q3S1A1_ROT rotation detector
AXIS_D0Q3S1 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S1A1 translation detector
AXIS_D0Q3S1 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S1A1_ROT
AXIS_D0Q3S1A1_F translation detector
AXIS_D0Q3S1A1 1 0 0 0 0 0 . .
AXIS_D0Q3S1A1_S translation detector
AXIS_D0Q3S1A1 0 1 0 0 0 0 . .
AXIS_D0Q3S2_ROT rotation detector
AXIS_D0Q3 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q3S2 translation detector
AXIS_D0Q3 . . . 10.9572375 -23.5830375 0.0
269.55191 AXIS_D0Q3S2_ROT
AXIS_D0Q3S2A0_ROT rotation detector
AXIS_D0Q3S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S2A0 translation detector
AXIS_D0Q3S2 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S2A0_ROT
AXIS_D0Q3S2A0_F translation detector
AXIS_D0Q3S2A0 1 0 0 0 0 0 . .
AXIS_D0Q3S2A0_S translation detector
AXIS_D0Q3S2A0 0 1 0 0 0 0 . .
AXIS_D0Q3S2A1_ROT rotation detector
AXIS_D0Q3S2 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S2A1 translation detector
AXIS_D0Q3S2 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S2A1_ROT
AXIS_D0Q3S2A1_F translation detector
AXIS_D0Q3S2A1 1 0 0 0 0 0 . .
AXIS_D0Q3S2A1_S translation detector
AXIS_D0Q3S2A1 0 1 0 0 0 0 . .
AXIS_D0Q3S3_ROT rotation detector
AXIS_D0Q3 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q3S3 translation detector
AXIS_D0Q3 . . . 34.4180375 -23.4818375 0.0
269.74206 AXIS_D0Q3S3_ROT
AXIS_D0Q3S3A0_ROT rotation detector
AXIS_D0Q3S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S3A0 translation detector
AXIS_D0Q3S3 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S3A0_ROT
AXIS_D0Q3S3A0_F translation detector
AXIS_D0Q3S3A0 1 0 0 0 0 0 . .
AXIS_D0Q3S3A0_S translation detector
AXIS_D0Q3S3A0 0 1 0 0 0 0 . .
AXIS_D0Q3S3A1_ROT rotation detector
AXIS_D0Q3S3 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S3A1 translation detector
AXIS_D0Q3S3 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S3A1_ROT
AXIS_D0Q3S3A1_F translation detector
AXIS_D0Q3S3A1 1 0 0 0 0 0 . .
AXIS_D0Q3S3A1_S translation detector
AXIS_D0Q3S3A1 0 1 0 0 0 0 . .
AXIS_D0Q3S4_ROT rotation detector
AXIS_D0Q3 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q3S4 translation detector
AXIS_D0Q3 . . . -24.1283625 -11.5336375 0.0
359.81971 AXIS_D0Q3S4_ROT
AXIS_D0Q3S4A0_ROT rotation detector
AXIS_D0Q3S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S4A0 translation detector
AXIS_D0Q3S4 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S4A0_ROT
AXIS_D0Q3S4A0_F translation detector
AXIS_D0Q3S4A0 1 0 0 0 0 0 . .
AXIS_D0Q3S4A0_S translation detector
AXIS_D0Q3S4A0 0 1 0 0 0 0 . .
AXIS_D0Q3S4A1_ROT rotation detector
AXIS_D0Q3S4 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S4A1 translation detector
AXIS_D0Q3S4 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S4A1_ROT
AXIS_D0Q3S4A1_F translation detector
AXIS_D0Q3S4A1 1 0 0 0 0 0 . .
AXIS_D0Q3S4A1_S translation detector
AXIS_D0Q3S4A1 0 1 0 0 0 0 . .
AXIS_D0Q3S5_ROT rotation detector
AXIS_D0Q3 0.0 0.0 1.0 0 0 0 . .
AXIS_D0Q3S5 translation detector
AXIS_D0Q3 . . . -24.1701625 -34.9548375 0.0
359.99883 AXIS_D0Q3S5_ROT
AXIS_D0Q3S5A0_ROT rotation detector
AXIS_D0Q3S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S5A0 translation detector
AXIS_D0Q3S5 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S5A0_ROT
AXIS_D0Q3S5A0_F translation detector
AXIS_D0Q3S5A0 1 0 0 0 0 0 . .
AXIS_D0Q3S5A0_S translation detector
AXIS_D0Q3S5A0 0 1 0 0 0 0 . .
AXIS_D0Q3S5A1_ROT rotation detector
AXIS_D0Q3S5 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S5A1 translation detector
AXIS_D0Q3S5 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S5A1_ROT
AXIS_D0Q3S5A1_F translation detector
AXIS_D0Q3S5A1 1 0 0 0 0 0 . .
AXIS_D0Q3S5A1_S translation detector
AXIS_D0Q3S5A1 0 1 0 0 0 0 . .
AXIS_D0Q3S6_ROT rotation detector
AXIS_D0Q3 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q3S6 translation detector
AXIS_D0Q3 . . . -33.3089625 23.4474625 0.0
269.67299 AXIS_D0Q3S6_ROT
AXIS_D0Q3S6A0_ROT rotation detector
AXIS_D0Q3S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S6A0 translation detector
AXIS_D0Q3S6 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S6A0_ROT
AXIS_D0Q3S6A0_F translation detector
AXIS_D0Q3S6A0 1 0 0 0 0 0 . .
AXIS_D0Q3S6A0_S translation detector
AXIS_D0Q3S6A0 0 1 0 0 0 0 . .
AXIS_D0Q3S6A1_ROT rotation detector
AXIS_D0Q3S6 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S6A1 translation detector
AXIS_D0Q3S6 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S6A1_ROT
AXIS_D0Q3S6A1_F translation detector
AXIS_D0Q3S6A1 1 0 0 0 0 0 . .
AXIS_D0Q3S6A1_S translation detector
AXIS_D0Q3S6A1 0 1 0 0 0 0 . .
AXIS_D0Q3S7_ROT rotation detector
AXIS_D0Q3 -0.0 -0.0 -1.0 0 0 0 . .
AXIS_D0Q3S7 translation detector
AXIS_D0Q3 . . . -10.0032625 23.4826625 0.0
269.67561 AXIS_D0Q3S7_ROT
AXIS_D0Q3S7A0_ROT rotation detector
AXIS_D0Q3S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S7A0 translation detector
AXIS_D0Q3S7 . . . -10.835 0.0 0.0 0.0 AXIS_D0Q3S7A0_ROT
AXIS_D0Q3S7A0_F translation detector
AXIS_D0Q3S7A0 1 0 0 0 0 0 . .
AXIS_D0Q3S7A0_S translation detector
AXIS_D0Q3S7A0 0 1 0 0 0 0 . .
AXIS_D0Q3S7A1_ROT rotation detector
AXIS_D0Q3S7 0.0 0.0 0.0 0 0 0 . .
AXIS_D0Q3S7A1 translation detector
AXIS_D0Q3S7 . . . 10.835 0.0 0.0 0.0 AXIS_D0Q3S7A1_ROT
AXIS_D0Q3S7A1_F translation detector
AXIS_D0Q3S7A1 1 0 0 0 0 0 . .
AXIS_D0Q3S7A1_S translation detector
AXIS_D0Q3S7A1 0 1 0 0 0 0 . .
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends, unless
_axis.rotation_axis is
specified, in which case, _axis.rotation_axis is
next outermost and _axis.depends_on is second
outermost.
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 implicit
_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.equipment_component
_item_description.description
; The value of _axis.equipment_component specifies
an arbitrary identifier of a component of the equipment to which
the axis belongs, such as 'detector_arm' or 'detector_module'.
;
_item.name '_axis.equipment_component'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
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.rotation
_item_description.description
; The value of _axis.rotation specifies
the fixed base rotation angle for _axis.rotation_axis
to which the value of any frame-by-frame setting, if any, should
be added. Normally, ony the fixed value would be given.
;
_item.name '_axis.rotation'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code degrees
save_
save__axis.rotation_axis
_item_description.description
; The value of _axis.rotation_axis specifies
and optional addtional dependency for this axis to be applied
after applying _axis.depends_on.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.rotation_axis'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
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_
save__axis.variant
_item_description.description
; The value of _axis.variant gives the variant
to which the given AXIS row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_axis.variant'
_item.category_id axis
_item.mandatory_code implicit
_item_type.code code
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
_category.NX_mapping_details
;
_diffrn_data_frame.array_id ARRAYID
_diffrn_data_frame.array_section_id SECTIONID
_diffrn_data_frame.binary_id BINID
_diffrn_data_frame.center_fast CENF
_diffrn_data_frame.center_slow CENS
_diffrn_data_frame.center_units UNITS
_diffrn_data_frame.detector_element_id ELEMENTID
_diffrn_data_frame.id FRAMEID
_diffrn_data_frame.details DETAILS
-->
/CBF_diffrn_scan__SCANID:NXentry
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/CBF_diffrn_data_frame__section_id=[SECTIONIDARRAY]
/CBF_diffrn_data_frame__binary_id=[BINARYIDARRAY]
/CBF_diffrn_data_frame__center_fast_slow=[CENTERARRAY]
@units="UNITS"
/CBF_diffrn_data_frame__details=["DETAILSARRAY"]
inserts either ARRAYID (if not SECTIONID is specified or the SECTIONID
into the element of SECTIONIDARRY for this frame and for this detector element (see below)
inserts BINID
into the element of BINARYIDARRAY for this frame and for this detector element (see below)
inserts CENF
into the element of CENTERARRAY for this frame, for this detector element
and for the fast center (see below)
inserts CENS
into element of CENTERARRAY for this frame, for this detector element
and for the slow center (see below)
only one CENTERARRY unit is provided. If there is variation, the values in
CENTERARRAY should be rescaled to uniform units.
_diffrn_data_frame.detector_element_id ELEMENTID -->
ELEMENTID used to index into the arrays of this category by the ordinal of
the matching ELEMENTID in DIFFRN_DETECTOR_ELEMENT__id for the fast index
FRAMEID used to index into the arrays of this category by the ordinal of
the matching ELEMENTID in DIFFRN_DETECTOR_ELEMENT__id for the slow index
by matching FRAMEID against _diffrn_scan_frame.frame_id and using
_diffrn_scan_frame.frame_number from the same row.
inserts DETAILS
into the element of DETAILSARRAY for this frame and for this detector element (see below)
The arrays created in the mapping have a slow index of the number of frames
and a fast index of the number of detector elements. There is a middle index
for CENTERARRAY in the order fast and then slow.
;
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
'_diffrn_data_frame.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'diffrn_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.array_section_id
_item_description.description
; This item is a pointer to _array_structure_list_section.id
in the ARRAY_STRUCTURE_LIST_SECTION category.
;
_item.name '_diffrn_data_frame.array_section_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_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_
save__diffrn_data_frame.id
_item_description.description
; The value of _diffrn_data_frame.id must uniquely identify
each complete frame of data.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_data_frame.id' diffrn_data_frame yes
'_diffrn_refln.frame_id' diffrn_refln yes
'_diffrn_scan.frame_id_start' diffrn_scan yes
'_diffrn_scan.frame_id_end' diffrn_scan yes
'_diffrn_scan_frame.frame_id' diffrn_scan_frame yes
'_diffrn_scan_frame_axis.frame_id'
diffrn_scan_frame_axis
yes
'_diffrn_scan_frame_monitor.frame_id'
diffrn_scan_frame_monitor
implicit
_item_aliases.alias_name '_diffrn_frame_data.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_refln.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_start' '_diffrn_data_frame.id'
'_diffrn_scan.frame_id_end' '_diffrn_data_frame.id'
'_diffrn_scan_frame.frame_id' '_diffrn_data_frame.id'
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_data_frame.id'
'_diffrn_scan_frame_monitor.frame_id'
'_diffrn_data_frame.id'
save_
save__diffrn_data_frame.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
This is an appropriate location in which to record
information from vendor headers as presented in those
headers, but it should never be used as a substitute
for providing the fully parsed information within
the appropriate imgCIF/CBF categories.
Normally, when a conversion from a miniCBF has been done
the data from '_array_data.header_convention'
should be transferred to this data item and
'_array_data.header_convention'
should be removed.
;
_item.name '_diffrn_data_frame.details'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_frame_data.details'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.4
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
;
HEADER_BYTES = 512;
DIM = 2;
BYTE_ORDER = big_endian;
TYPE = unsigned_short;
SIZE1 = 3072;
SIZE2 = 3072;
PIXEL_SIZE = 0.102588;
BIN = 2x2;
DETECTOR_SN = 901;
TIME = 29.945155;
DISTANCE = 200.000000;
PHI = 85.000000;
OSC_START = 85.000000;
OSC_RANGE = 1.000000;
WAVELENGTH = 0.979381;
BEAM_CENTER_X = 157.500000;
BEAM_CENTER_Y = 157.500000;
PIXEL SIZE = 0.102588;
OSCILLATION RANGE = 1;
EXPOSURE TIME = 29.9452;
TWO THETA = 0;
BEAM CENTRE = 157.5 157.5;
;
; Example of header information extracted from an ADSC Quantum
315 detector header by CBFlib_0.7.6. Image provided by Chris
Nielsen of ADSC from a data collection at SSRL beamline 1-5.
;
save_
save__diffrn_data_frame.variant
_item_description.description
; The value of _diffrn_data_frame.variant gives the variant
to which the given DIFFRN_DATA_FRAME row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_data_frame.variant'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_type.code code
save_
##########################################################################
# The following is a restatement of the mmCIF DIFFRN_DETECTOR, #
# DIFFRN_MEASUREMENT and DIFFRN_RADIATION categories, modified for #
# the CBF/imgCIF extensions #
##########################################################################
###################
# DIFFRN_DETECTOR #
###################
save_diffrn_detector
_category.description
; Data items in the DIFFRN_DETECTOR category describe the
detector used to measure the scattered radiation, including
any analyser and post-sample collimation.
;
_category.id diffrn_detector
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_detector.diffrn_id DIFFRNID
_diffrn_detector.id DETECTORNAME
_diffrn_detector.details DETAILS
_diffrn_detector.detector DETECTOR
_diffrn_detector.dtime DTIME
_diffrn_detector.gain_setting GAINSETTING
_diffrn_detector.number_of_axes NAXES
_diffrn_detector.type DETTYPE
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/CBF_diffrn_id="DIFFRNID"
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/details="DETAILS"
/type="DETECTOR"
/deadtime=DTIME
/number_of_axes=NAXES
/decription="DETTYPE"
/gain_setting="GAINSETTING"
;
loop_
_category_key.name '_diffrn_detector.diffrn_id'
'_diffrn_detector.id'
'_diffrn_detector.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP.
;
;
_diffrn_detector.diffrn_id 'd1'
_diffrn_detector.detector 'multiwire'
_diffrn_detector.type 'Siemens'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector.details
_item_description.description
; A description of special aspects of the radiation detector.
;
_item.name '_diffrn_detector.details'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case 'slow mode'
save_
save__diffrn_detector.detector
_item_description.description
; The general class of the radiation detector.
;
_item.name '_diffrn_detector.detector'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector'
cifdic.c91
1.0
'_diffrn_detector'
cif_core.dic
2.0
_item_type.code text
loop_
_item_examples.case 'photographic film'
'scintillation counter'
'CCD plate'
'BF~3~ counter'
save_
save__diffrn_detector.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
The value of _diffrn.id uniquely defines a set of
diffraction data.
;
_item.name '_diffrn_detector.diffrn_id'
_item.category_id diffrn_detector
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector.dtime
_item_description.description
; The deadtime in microseconds of the detector(s) used to
measure the diffraction intensities.
;
_item.name '_diffrn_detector.dtime'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_aliases.alias_name
_item_aliases.dictionary
_item_aliases.version '_diffrn_radiation_detector_dtime'
cifdic.c91
1.0
'_diffrn_detector_dtime'
cif_core.dic
2.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code microseconds
save_
save__diffrn_detector.id
_item_description.description
; The value of _diffrn_detector.id must uniquely identify
each detector used to collect each diffraction data set.
If the value of _diffrn_detector.id is not given, it is
implicitly equal to the value of
_diffrn_detector.diffrn_id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector.id' diffrn_detector implicit
'_diffrn_detector_axis.detector_id'
diffrn_detector_axis yes
'_diffrn_scan_frame_monitor.detector_id'
diffrn_scan_frame_monitor yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_detector_axis.detector_id'
'_diffrn_detector.id'
'_diffrn_scan_frame_monitor.detector_id'
'_diffrn_detector.id'
_item_type.code code
save_
save__diffrn_detector.layer_thickness
_item_description.description
; The thickness in mm of the sensing layer of the detector
for use in anglular corrections.
;
_item.name '_diffrn_detector.layer_thickness'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector.gain_setting
_item_description.description
; The gain setting for detector. This is a text string usually
reflecting a detector setting that may have a simple or very
complex relationship with the value of
_array_intensities.gain
and should not be used directly for computations without
further information.
This tag is provided for completeness in recording the settings
of an experiment using a dector with a panel-switch, jumper
or control command that allows a choice of gain settings.
;
_item.name '_diffrn_detector.gain_setting'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_type.code text
save_
save__diffrn_detector.number_of_axes
_item_description.description
; The value of _diffrn_detector.number_of_axes gives the
number of axes of the positioner for the detector identified
by _diffrn_detector.id.
The word 'positioner' is a general term used in
instrumentation design for devices that are used to change
the positions of portions of apparatus by linear
translation, rotation or combinations of such motions.
Axes which are used to provide a coordinate system for the
face of an area detetctor should not be counted for this
data item.
The description of each axis should be provided by entries
in DIFFRN_DETECTOR_AXIS.
;
_item.name '_diffrn_detector.number_of_axes'
_item.category_id diffrn_detector
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
save__diffrn_detector.type
_item_description.description
; The make, model or name of the detector device used.
;
_item.name '_diffrn_detector.type'
_item.category_id diffrn_detector
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_detector_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
save_
save__diffrn_detector.variant
_item_description.description
; The value of _diffrn_detector.variant gives the variant
to which the given DIFFRN_DETECTOR row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector.variant'
_item.category_id diffrn_detector
_item.mandatory_code implicit
_item_type.code code
save_
########################
# DIFFRN_DETECTOR_AXIS #
########################
save_diffrn_detector_axis
_category.description
; Data items in the DIFFRN_DETECTOR_AXIS category associate
axes with detectors.
;
_category.id diffrn_detector_axis
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_detector_axis.axis_id AXISID -->
_diffrn_detector_axis.detector_id DETECTORNAME -->
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/transformations:NXtransformations
/AXISID=[]
This information normally will duplicate information obtained from
the ARRAY_STRUCTURE_LIST_AXIS.
;
loop_
_category_key.name '_diffrn_detector_axis.detector_id'
'_diffrn_detector_axis.axis_id'
'_diffrn_detector_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_detector_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_detector_axis.axis_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_axis.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
This item was previously named _diffrn_detector_axis.id
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_detector_axis.detector_id'
_item.category_id diffrn_detector_axis
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_detector_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_detector_axis.variant
_item_description.description
; The value of _diffrn_detector_axis.variant gives the variant
to which the given DIFFRN_DETECTOR_AXIS row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector_axis.variant'
_item.category_id diffrn_detector_axis
_item.mandatory_code implicit
_item_type.code code
save_
###########################
# DIFFRN_DETECTOR_ELEMENT #
###########################
save_diffrn_detector_element
_category.description
; Data items in the DIFFRN_DETECTOR_ELEMENT category record
the details about spatial layout and other characteristics
of each element of a detector which may have multiple elements.
In most cases, giving more detailed information
in ARRAY_STRUCTURE_LIST and ARRAY_STRUCTURE_LIST_AXIS
is preferable to simply providing the centre of the
detector element.
;
_category.id diffrn_detector_element
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_detector_element.id ELEMENTID
_diffrn_detector_element.detector_id DETECTORNAME
_diffrn_detector_element.reference_center_fast RCF
_diffrn_detector_element.reference_center_slow RCS
_diffrn_detector_element.reference_center_units UNITS
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/CBF_diffrn_id="DIFFRNID"
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/beam_center_x=[RCS] (converted from UNITS as needed)
@units=mm
/beam_center_y=[RCF] (converted from UNITS as needed)
@units=mm
/CBF_diffrn_detector_element__id="ELEMENTID1:ELEMENTID2:..."
/CBF_diffrn_detector_element__reference_center_fast=[RCF1,RCF2,...]
/CBF_diffrn_detector_element__reference_center_slow=[RCS1,RCS2,...]
/CBF_diffrn_detector_element__id="UNITS1:UNITS2:..."
inserts ELEMENTID into the colon-separated list of element IDs
inserts RCF into the array of reference centers
inserts RCS into the array of reference centers
inserts ELEMENTID into the colon-separated list of units
;
loop_
_category_key.name '_diffrn_detector_element.id'
'_diffrn_detector_element.detector_id'
'_diffrn_detector_element.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Detector d1 is composed of four CCD detector elements,
each 200 mm by 200 mm, arranged in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
;
;
loop_
_diffrn_detector_element.detector_id
_diffrn_detector_element.id
_diffrn_detector_element.reference_center_fast
_diffrn_detector_element.reference_center_slow
_diffrn_detector_element.reference_center_units
d1 d1_ccd_1 201.5 201.5 mm
d1 d1_ccd_2 -1.8 201.5 mm
d1 d1_ccd_3 201.6 -1.4 mm
d1 d1_ccd_4 -1.7 -1.5 mm
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_detector_element.id
_item_description.description
; The value of _diffrn_detector_element.id must uniquely
identify each element of a detector.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_detector_element.id'
diffrn_detector_element
yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.detector_element_id'
'_diffrn_detector_element.id'
save_
save__diffrn_detector_element.detector_id
_item_description.description
; This item is a pointer to _diffrn_detector.id
in the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_detector_element.detector_id'
_item.category_id diffrn_detector_element
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_detector_element.reference_center_fast
_item_description.description
; The value of _diffrn_detector_element.reference_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_detector_element.reference_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 all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value given whould be
representive of the beam center as determined from the ensemble
of settings.
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_detector_element.reference_center_fast'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_slow
_item_description.description
; The value of _diffrn_detector_element.reference_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_detector_element.reference_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 all settings of the detector
positioner should be at their reference settings. If more than
one reference setting has been used the value givien whould be
representive of the beam center as determined from the ensemble
of settings.
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_detector_element.reference_center_slow'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_detector_element.reference_center_units
_item_description.description
; The value of _diffrn_detector_element.reference_center_units
specifies the units in which the values of
'_diffrn_detector_element.reference_center_fast' and
'_diffrn_detector_element.reference_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_detector_element.reference_center_units'
_item.category_id diffrn_detector_element
_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_detector_element.variant
_item_description.description
; The value of _diffrn_detector_element.variant gives the variant
to which the given DIFFRN_DETECTOR_ELEMENT row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_detector_element.variant'
_item.category_id diffrn_detector_element
_item.mandatory_code implicit
_item_type.code code
save_
########################
## DIFFRN_MEASUREMENT ##
########################
save_diffrn_measurement
_category.description
; Data items in the DIFFRN_MEASUREMENT category record details
about the device used to orient and/or position the crystal
during data measurement and the manner in which the
diffraction data were measured.
;
_category.id diffrn_measurement
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_measurement.diffrn_id DIFFRNID
_diffrn_measurement.details DETAILS
_diffrn_measurement.device DEVICE
_diffrn_measurement.device_details DEVDETAILS
_diffrn_measurement.device_type DEVTYPE
_diffrn_measurement.id GONIOMETER
_diffrn_measurement.method METHOD
_diffrn_measurement.number_of_axes NUMBER
_diffrn_measurement.sample_detector_distance DIST
_diffrn_measurement.sample_detector_voffset VOFST
_diffrn_measurement.specimen_support SPECSPRT
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID
/CBF_diffrn_id="DIFFRNID"
/instrument:NXinstrument
/CBF_diffrn_measurement__GONIOMETER:NXgoniometer
/details="DETAILS"
/local_name="DEVICE"
/description="DEVDETAILS"
/type="DEVTYPE"
/CBF_diffrn_measurement__method="METHOD"
/number_of_axes=NUMBER
/CBF_diffrn_measurement__specimen_support="SPECSPRT"
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/distance=DIST
@units="mm"
/CBF_diffrn_measurement__sample_detector_voffset=VOFST
@units="mm"
;
loop_
_category_key.name '_diffrn_measurement.device'
'_diffrn_measurement.diffrn_id'
'_diffrn_measurement.id'
'_diffrn_measurement.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_measurement.diffrn_id 'd1'
_diffrn_measurement.device '3-circle camera'
_diffrn_measurement.device_type 'Supper model X'
_diffrn_measurement.device_details 'none'
_diffrn_measurement.method 'omega scan'
_diffrn_measurement.details
; 440 frames, 0.20 degrees, 150 sec, detector distance 12 cm, detector
angle 22.5 degrees
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_measurement.diffrn_id 's1'
_diffrn_measurement.device_type 'Philips PW1100/20 diffractometer'
_diffrn_measurement.method 'theta/2theta (\q/2\q)'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_measurement.device
_item_description.description
; The general class of goniometer or device used to support
and orient the specimen.
If the value of _diffrn_measurement.device is not given,
it is implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.device' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_device'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement.device'
_item_aliases.alias_name '_diffrn_measurement_device'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '3-circle camera'
'4-circle camera'
'kappa-geometry camera'
'oscillation camera'
'precession camera'
save_
save__diffrn_measurement.device_details
_item_description.description
; A description of special aspects of the device used to
measure the diffraction intensities.
;
_item.name '_diffrn_measurement.device_details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; commercial goniometer modified locally to
allow for 90\% \t arc
;
save_
save__diffrn_measurement.device_type
_item_description.description
; The make, model or name of the measurement device
(goniometer) used.
;
_item.name '_diffrn_measurement.device_type'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_device_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Supper model q'
'Huber model r'
'Enraf-Nonius model s'
'home-made'
save_
save__diffrn_measurement.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_measurement.diffrn_id'
_item.category_id diffrn_measurement
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement.details
_item_description.description
; A description of special aspects of the intensity
measurement.
;
_item.name '_diffrn_measurement.details'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_details'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
; 440 frames, 0.20 degrees, 150 sec, detector
distance 12 cm, detector angle 22.5 degrees
;
save_
save__diffrn_measurement.id
_item_description.description
; The value of _diffrn_measurement.id must uniquely identify
the set of mechanical characteristics of the device used to
orient and/or position the sample used during the collection
of each diffraction data set.
If the value of _diffrn_measurement.id is not given, it is
implicitly equal to the value of
_diffrn_measurement.diffrn_id.
Either _diffrn_measurement.device or
_diffrn_measurement.id may be used to link to other
categories. If the experimental setup admits multiple
devices, then _diffrn_measurement.id is used to provide
a unique link.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_measurement.id' diffrn_measurement implicit
'_diffrn_measurement_axis.measurement_id'
diffrn_measurement_axis implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement.id'
_item_type.code code
save_
save__diffrn_measurement.method
_item_description.description
; Method used to measure intensities.
;
_item.name '_diffrn_measurement.method'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_method'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
_item_examples.case
'profile data from theta/2theta (\q/2\q) scans'
save_
save__diffrn_measurement.number_of_axes
_item_description.description
; The value of _diffrn_measurement.number_of_axes gives the
number of axes of the positioner for the goniometer or
other sample orientation or positioning device identified
by _diffrn_measurement.id.
The description of the axes should be provided by entries in
DIFFRN_MEASUREMENT_AXIS.
;
_item.name '_diffrn_measurement.number_of_axes'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 1
1 1
_item_type.code int
save_
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
save__diffrn_measurement.sample_detector_distance
_item_description.description
; The value of _diffrn_measurement.sample_detector_distance gives
the unsigned distance in millimetres from the sample to the
detector along the beam.
;
_item.name '_diffrn_measurement.sample_detector_distance'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_measurement.sample_detector_voffset
_item_description.description
; The value of _diffrn_measurement.sample_detector_voffset gives
the signed distance in millimetres in the vertical
direction (positive for up) from the center of
the beam to the center of the detector.
;
_item.name '_diffrn_measurement.sample_detector_voffset'
_item.category_id diffrn_measurement
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . .
. .
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_measurement.specimen_support
_item_description.description
; The physical device used to support the crystal during data
collection.
;
_item.name '_diffrn_measurement.specimen_support'
_item.category_id diffrn_measurement
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_measurement_specimen_support'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'glass capillary'
'quartz capillary'
'fiber'
'metal loop'
save_
save__diffrn_measurement.variant
_item_description.description
; The value of _diffrn_measurement.variant gives the variant
to which the given DIFFRN_MEASUREMENT row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_measurement.variant'
_item.category_id diffrn_measurement
_item.mandatory_code implicit
_item_type.code code
save_
###########################
# DIFFRN_MEASUREMENT_AXIS #
###########################
save_diffrn_measurement_axis
_category.description
; Data items in the DIFFRN_MEASUREMENT_AXIS category associate
axes with goniometers.
;
_category.id diffrn_measurement_axis
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_measurement_axis.axis_id AXISID
_diffrn_measurement_axis.measurement_device DEVICE
_diffrn_measurement_axis.measurement_id GONIOMETER
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID
/CBF_diffrn_id="DIFFRNID"
/sample:Nxsample
/transformations:NXtransformations
/AXISID=[]
/instrument:NXinstrument
/CBF_diffrn_measurement__GONIOMETER:NXgoniometer
/CBF_diffrn_measurement__device="DEVICE"
;
loop_
_category_key.name
'_diffrn_measurement_axis.measurement_device'
'_diffrn_measurement_axis.measurement_id'
'_diffrn_measurement_axis.axis_id'
'_diffrn_measurement_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_measurement_axis.axis_id
_item_description.description
; This data item is a pointer to _axis.id in
the AXIS category.
;
_item.name '_diffrn_measurement_axis.axis_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_measurement_axis.measurement_device
_item_description.description
; This data item is a pointer to _diffrn_measurement.device
in the DIFFRN_MEASUREMENT category.
;
_item.name
'_diffrn_measurement_axis.measurement_device'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code text
save_
save__diffrn_measurement_axis.measurement_id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
This item was previously named _diffrn_measurement_axis.id,
which is now a deprecated name. The old name is
provided as an alias but should not be used for new work.
;
_item.name '_diffrn_measurement_axis.measurement_id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_measurement_axis.id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_measurement_axis.variant
_item_description.description
; The value of _diffrn_measurement_axis.variant gives the variant
to which the given DIFFRN_MEASUREMENT_AXIS row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_measurement_axis.variant'
_item.category_id diffrn_measurement_axis
_item.mandatory_code implicit
_item_type.code code
save_
####################
# DIFFRN_RADIATION #
####################
save_diffrn_radiation
_category.description
; Data items in the DIFFRN_RADIATION category describe
the radiation used for measuring diffraction intensities,
its collimation and monochromatization before the sample.
Post-sample treatment of the beam is described by data
items in the DIFFRN_DETECTOR category.
;
_category.id diffrn_radiation
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_radiation.collimation COLLIMATION
_diffrn_radiation.diffrn_id DIFFRNID
_diffrn_radiation.div_x_source DIVX
_diffrn_radiation.div_y_source DIVY
_diffrn_radiation.div_x_y_source DIVXY
_diffrn_radiation.filter_edge' ABSEDGE
_diffrn_radiation.inhomogeneity HWIDTH
_diffrn_radiation.monochromator MONOCHROMATOR
_diffrn_radiation.polarisn_norm POLNANG
_diffrn_radiation.polarisn_ratio POLRAT
_diffrn_radiation.polarizn_source_norm POLSNANG
_diffrn_radiation.polarizn_source_ratio POLSRAT
_diffrn_radiation.polarizn_Stokes_I SVECI
_diffrn_radiation.polarizn_Stokes_Q SVECQ
_diffrn_radiation.polarizn_Stokes_U SVECU
_diffrn_radiation.polarizn_Stokes_V SVECV
_diffrn_radiation.polarisn_norm_esd POLNANGESD
_diffrn_radiation.polarisn_ratio_esd POLRATESD
_diffrn_radiation.polarizn_source_norm_esd POLSNANGESD
_diffrn_radiation.polarizn_source_ratio_esd POLSRATESD
_diffrn_radiation.polarizn_Stokes_I_esd SVECIESD
_diffrn_radiation.polarizn_Stokes_Q_esd SVECQESD
_diffrn_radiation.polarizn_Stokes_U_esd SVECUESD
_diffrn_radiation.polarizn_Stokes_V_esd SVECVESD
_diffrn_radiation.probe RADIATION
_diffrn_radiation.type SIEGBAHNTYPE
_diffrn_radiation.xray_symbol IUPACXRAYSYMB
_diffrn_radiation.wavelength_id ID
_diffrn_radiation_wavelength.id ID
_diffrn_radiation_wavelength.wavelength WAVELENGTH
_diffrn_radiation_wavelength.wt WEIGHT
_diffrn_scan_frame.polarizn_Stokes_I STOKESI
_diffrn_scan_frame.polarizn_Stokes_Q STOKESQ
_diffrn_scan_frame.polarizn_Stokes_U STOKESU
_diffrn_scan_frame.polarizn_Stokes_V STOKESV
_diffrn_scan_frame.polarizn_Stokes_I_esd STOKESIESD
_diffrn_scan_frame.polarizn_Stokes_Q_esd STOKESQESD
_diffrn_scan_frame.polarizn_Stokes_U_esd STOKESUESD
_diffrn_scan_frame.polarizn_Stokes_V_esd STOKESVESD
_diffrn_scan_frame.frame_number FRAMENO
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/sample:NXsample
/beam:NXbeam
/incident_divergence_x=DIVX
@units="degrees"
/incident_divergence_y=DIVY
@units="degrees"
/incident_divergence_xy=DIXXY
@units="degrees^2"
/CBF_diffrn_radiation_wavelength__wavelength_id=[WAVELENGTH_ID]
/incident_wavelength=[WAVELENGTH]
@units="A"
/weight=[WEIGHT]
/incident_polarisation_stokes_average=[SVECI,SVECQ,SVECU,SVECV]
/incident_polarisation_stokes_average_uncertainty=[SVECIESD,SVECQESD,SVECUESD,SVECVESD]
/incident_polarisation_stokes=[STOKESI,STOKESQ,STOKESU,STOKESV]
/incident_polarisation_stokes_uncertainty=[STOKESIESD,STOKESQESD,STOKESUESD,STOKESVESD]
@units="Watts/meter^2"
/CBF_diffrn_radiation__polarisn_norm=POLNANG
@units="deg"
/CBF_diffrn_radiation__polarisn_ratio=POLRAT
/CBF_diffrn_radiation__polarisn_norm_uncertainty=POLNANGESD
@units="deg"
/CBF_diffrn_radiation__polarisn_ratio_uncertainty=POLRATESD
/CBF_diffrn_radiation__polarisn_source_norm=POLSNANG
@units="deg"
/CBF_diffrn_radiation__polarizn_source_ratio=POLSRAT
/CBF_diffrn_radiation__polarisn_source_norm_uncertainty=POLSNANGESD
@units="deg"
/CBF_diffrn_radiation__polarizn_source_ratio_uncertainty=POLSRATESD
/CBF_diffrn_radiation__filter_edge=ABSEDGE
@units="angstroms"
/CBF_diffrn_radiation__inhomogeneity=HWIDTH
@units="mm"
/instrument:NXinstrument
/monchromator:NXmonochromator
/description="MONOCHROMATOR"
/source:NXsource
/probe="RADIATION"
/CBF_diffrn_radiation__type="SIEGBAHNTYPE"
/CBF_diffrn_radiation__xray_symbol="IUPACXRAYSYMB"
With the incident_polarisation_stokes array indexed by FRAMENO
;
loop_
_category_key.name '_diffrn_radiation.diffrn_id'
'_diffrn_radiation.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - based on PDB entry 5HVP and laboratory records for the
structure corresponding to PDB entry 5HVP
;
;
_diffrn_radiation.diffrn_id 'set1'
_diffrn_radiation.collimation '0.3 mm double pinhole'
_diffrn_radiation.monochromator 'graphite'
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.wavelength_id 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 - based on data set TOZ of Willis, Beckwith & Tozer
[Acta Cryst. (1991), C47, 2276-2277].
;
;
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.type 'Cu K\a'
_diffrn_radiation.monochromator 'graphite'
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_radiation.collimation
_item_description.description
; The collimation or focusing applied to the radiation.
;
_item.name '_diffrn_radiation.collimation'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_collimation'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case '0.3 mm double-pinhole'
'0.5 mm'
'focusing mirrors'
save_
save__diffrn_radiation.diffrn_id
_item_description.description
; This data item is a pointer to _diffrn.id in the DIFFRN
category.
;
_item.name '_diffrn_radiation.diffrn_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.div_x_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory X axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions of
photons in the XZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_x_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.div_y_source
_item_description.description
; Beam crossfire in degrees parallel to the laboratory Y axis
(see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the standard uncertainty (e.s.d.) of the directions
of photons in the YZ plane around the mean source beam
direction.
Note that for some synchrotrons this value is specified
in milliradians, in which case a conversion is needed.
To convert a value in milliradians to a value in degrees,
multiply by 0.180 and divide by \p.
;
_item.name '_diffrn_radiation.div_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.div_x_y_source
_item_description.description
; Beam crossfire correlation degrees^2^ between the
crossfire laboratory X-axis component and the crossfire
laboratory Y-axis component (see AXIS category).
This is a characteristic of the X-ray beam as it illuminates
the sample (or specimen) after all monochromation and
collimation.
This is the mean of the products of the deviations of the
direction of each photon in XZ plane times the deviations
of the direction of the same photon in the YZ plane
around the mean source beam direction. This will be zero
for uncorrelated crossfire.
Note that some synchrotrons, this value is specified in
milliradians^2^, in which case a conversion would be needed.
To go from a value in milliradians^2^ to a value in
degrees^2^, multiply by 0.180^2^ and divide by \p^2^.
;
_item.name '_diffrn_radiation.div_x_y_source'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_type.code float
_item_units.code degrees_squared
_item_default.value 0.0
save_
save__diffrn_radiation.filter_edge
_item_description.description
; Absorption edge in \%Angstroms of the radiation filter used.
;
_item.name '_diffrn_radiation.filter_edge'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_filter_edge'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__diffrn_radiation.inhomogeneity
_item_description.description
; Half-width in millimetres of the incident beam in the
direction perpendicular to the diffraction plane.
;
_item.name '_diffrn_radiation.inhomogeneity'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_inhomogeneity'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_radiation.monochromator
_item_description.description
; The method used to obtain monochromatic radiation. If a
monochromator crystal is used, the material and the
indices of the Bragg reflection are specified.
;
_item.name '_diffrn_radiation.monochromator'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_monochromator'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code text
loop_
_item_examples.case 'Zr filter'
'Ge 220'
'none'
'equatorial mounted graphite'
save_
save__diffrn_radiation.polarisn_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_norm'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
save_
save__diffrn_radiation.polarisn_norm_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarisn_norm,
the angle in degrees, as viewed from the specimen, between the
perpendicular component of the polarization and the diffraction
plane. See _diffrn_radiation_polarisn_ratio.
;
_item.name '_diffrn_radiation.polarisn_norm_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarisn_norm'
'associated_value'
save_
save__diffrn_radiation.polarisn_ratio
_item_description.description
; Polarization ratio of the diffraction beam incident on the
crystal. This is the ratio of the perpendicularly polarized to
the parallel polarized component of the radiation. The
perpendicular component forms an angle of
_diffrn_radiation.polarisn_norm to the normal to the
diffraction plane of the sample (i.e. the plane containing
the incident and reflected beams).
;
_item.name '_diffrn_radiation.polarisn_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarisn_ratio_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarisn_ratio,
the polarization ratio of the diffraction beam incident on the
crystal.
;
_item.name '_diffrn_radiation.polarisn_ratio_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_polarisn_ratio_esd'
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarisn_ratio'
'associated_value'
save_
save__diffrn_radiation.polarizn_source_norm
_item_description.description
; The angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
Note that this is the angle of polarization of the source
photons, either directly from a synchrotron beamline or
from a monochromater.
This differs from the value of
_diffrn_radiation.polarisn_norm
in that _diffrn_radiation.polarisn_norm refers to
polarization relative to the diffraction plane rather than
to the laboratory axis system.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane should be taken
as the XZ plane and the angle as 0.
See _diffrn_radiation.polarizn_source_ratio.
;
_item.name '_diffrn_radiation.polarizn_source_norm'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 90.0 90.0
90.0 -90.0
-90.0 -90.0
_item_type.code float
_item_units.code degrees
_item_default.value 0.0
save_
save__diffrn_radiation.polarizn_source_norm_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarizn_source_norm,
the angle in degrees, as viewed from the specimen, between
the normal to the polarization plane and the laboratory Y
axis as defined in the AXIS category.
;
_item.name
'_diffrn_radiation.polarizn_source_norm_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code degrees
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarizn_source_norm'
'associated_value'
save_
save__diffrn_radiation.polarizn_source_ratio
_item_description.description
; (Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
In the case of an unpolarized beam, or a beam with true
circular polarization, in which no single plane of
polarization can be determined, the plane is to be taken
as the XZ plane and the normal is parallel to the Y axis.
Thus, if there was complete polarization in the plane of
polarization, the value of
_diffrn_radiation.polarizn_source_ratio would be 1, and
for an unpolarized beam
_diffrn_radiation.polarizn_source_ratio would have a
value of 0.
If the X axis has been chosen to lie in the plane of
polarization, this definition will agree with the definition
of 'MONOCHROMATOR' in the Denzo glossary, and values of near
1 should be expected for a bending-magnet source. However,
if the X axis were perpendicular to the polarization plane
(not a common choice), then the Denzo value would be the
negative of _diffrn_radiation.polarizn_source_ratio.
See http://www.hkl-xray.com for information on Denzo and
Otwinowski & Minor (1997).
This differs both in the choice of ratio and choice of
orientation from _diffrn_radiation.polarisn_ratio, which,
unlike _diffrn_radiation.polarizn_source_ratio, is
unbounded.
Reference: Otwinowski, Z. & Minor, W. (1997). 'Processing of
X-ray diffraction data collected in oscillation mode.' Methods
Enzymol. 276, 307-326.
;
_item.name '_diffrn_radiation.polarizn_source_ratio'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum 1.0 1.0
1.0 -1.0
-1.0 -1.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_source_ratio_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarizn_source_ratio,
(Ip-In)/(Ip+In), where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared)
of the electric vector in the plane of the normal to the
plane of polarization.
;
_item.name '_diffrn_radiation.polarizn_source_ratio_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarizn_source_ratio'
'associated_value'
save_
save__diffrn_radiation.polarizn_Stokes_I
_item_description.description
;
Ip+In+Inp, where where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization,
In is the intensity (amplitude squared) of the electric vector
in the plane of the normal to the plane of polarization,
and Inp is the intensity (amplitude squared) of the non-
polarized (incoherent) electric vector.
This is an average or other representative sample of the
scan.
This is the first of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
Note that, if the polarized intensity Ip+In is required,
(Ip+In)^2 is the sum of Q^2+U^2+V^2.
;
_item.name '_diffrn_radiation.polarizn_Stokes_I'
_item.category_id diffrn_radiation
_item.mandatory_code implicit
_item_default.value 1.0
loop_
_item_range.maximum
_item_range.minimum
. 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_radiation.polarizn_Stokes_I_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarizn_Stokes_I,
Ip+In+Inp, where where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization,
In is the intensity (amplitude squared) of the electric vector
in the plane of the normal to the plane of polarization,
and Inp is the intensity (amplitude squared) of the non-
polarized (incoherent) electric vector.
;
_item.name '_diffrn_radiation.polarizn_Stokes_I_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarizn_Stokes_I'
'associated_value'
save_
save__diffrn_radiation.polarizn_Stokes_Q
_item_description.description
;
(Ip-In)*cos(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
This is an average or other representative sample of the
scan.
This is the second of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
;
_item.name '_diffrn_radiation.polarizn_Stokes_Q'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_type.code float
save_
save__diffrn_radiation.polarizn_Stokes_Q_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarizn_Stokes_Q,
(Ip-In)*cos(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
;
_item.name '_diffrn_radiation.polarizn_Stokes_Q_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarizn_Stokes_Q'
'associated_value'
save_
save__diffrn_radiation.polarizn_Stokes_U
_item_description.description
;
(Ip-In)*sin(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
This is an average or other representative sample of the
scan.
This is the third of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
;
_item.name '_diffrn_radiation.polarizn_Stokes_U'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_type.code float
save_
save__diffrn_radiation.polarizn_Stokes_U_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarizn_Stokes_U,
(Ip-In)*sin(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
;
_item.name '_diffrn_radiation.polarizn_Stokes_U_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarizn_Stokes_U'
'associated_value'
save_
save__diffrn_radiation.polarizn_Stokes_V
_item_description.description
;
+/-2*sqrt(IpIn), with a + sign for right-handed circular
polarization, where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
This is an average or other representative sample of the
scan.
This is the fourth of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
;
_item.name '_diffrn_radiation.polarizn_Stokes_V'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_type.code float
save_
save__diffrn_radiation.polarizn_Stokes_V_esd
_item_description.description
; The setimated standard deviation of
_diffrn_radiation.polarizn_Stokes_V,
+/-2*sqrt(IpIn), with a + sign for right-handed circular
polarization, where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
;
_item.name '_diffrn_radiation.polarizn_Stokes_V_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_radiation.polarizn_Stokes_V'
'associated_value'
save_
save__diffrn_radiation.probe
_item_description.description
; Name of the type of radiation used. It is strongly
recommended that this be given so that the
probe radiation is clearly specified.
;
_item.name '_diffrn_radiation.probe'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_probe'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value 'X-ray'
'neutron'
'electron'
'gamma'
save_
save__diffrn_radiation.type
_item_description.description
; The nature of the radiation. This is typically a description
of the X-ray wavelength in Siegbahn notation.
;
_item.name '_diffrn_radiation.type'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_type'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_examples.case 'CuK\a'
'Cu K\a~1~'
'Cu K-L~2,3~'
'white-beam'
save_
save__diffrn_radiation.xray_symbol
_item_description.description
; The IUPAC symbol for the X-ray wavelength for the probe
radiation.
;
_item.name '_diffrn_radiation.xray_symbol'
_item.category_id diffrn_radiation
_item.mandatory_code no
_item_aliases.alias_name '_diffrn_radiation_xray_symbol'
_item_aliases.dictionary cif_core.dic
_item_aliases.version 2.0.1
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail 'K-L~3~'
'K\a~1~ in older Siegbahn notation'
'K-L~2~'
'K\a~2~ in older Siegbahn notation'
'K-M~3~'
'K\b~1~ in older Siegbahn notation'
'K-L~2,3~'
'use where K-L~3~ and K-L~2~ are not resolved'
save_
save__diffrn_radiation.wavelength_id
_item_description.description
; This data item is a pointer to
_diffrn_radiation_wavelength.id in the
DIFFRN_RADIATION_WAVELENGTH category.
;
_item.name '_diffrn_radiation.wavelength_id'
_item.category_id diffrn_radiation
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_radiation.variant
_item_description.description
; The value of _diffrn_radiation.variant gives the variant
to which the given DIFFRN_RADIATION row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_radiation.variant'
_item.category_id diffrn_radiation
_item.mandatory_code implicit
_item_type.code code
save_
################
# DIFFRN_REFLN #
################
save_diffrn_refln
_category.description
; This category redefinition has been added to extend the key of
the standard DIFFRN_REFLN category.
Data items in the DIFFRN_REFLN category record details about
the intensities in the diffraction data set
identified by _diffrn_refln.diffrn_id.
The DIFFRN_REFLN data items refer to individual intensity
measurements and must be included in looped lists.
The DIFFRN_REFLNS data items specify the parameters that apply
to all intensity measurements in the particular diffraction
data set identified by _diffrn_reflns.diffrn_id and
_diffrn_refln.frame_id
;
_category.id diffrn_refln
_category.mandatory_code no
_category.NX_mapping_details
;
This category will be addressed at a future date.
;
loop_
_category_key.name '_diffrn_refln.diffrn_id'
'_diffrn_refln.id'
'_diffrn_refln.frame_id'
'_diffrn_refln.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_refln.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_refln.frame_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_refln.variant
_item_description.description
; The value of _diffrn_refln.variant gives the variant
to which the given DIFFRN_REFLN row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_refln.variant'
_item.category_id diffrn_refln
_item.mandatory_code implicit
_item_type.code code
save_
save__diffrn_refln.id
_item_description.description
; This item is a placeholder for the definition in the PDBx/mmCIF dictionary.
;
_item.name '_diffrn_refln.id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_refln.diffrn_id
_item_description.description
; This item is a placeholder for the definition in the PDBx/mmCIF dictionary
;
_item.name '_diffrn_refln.diffrn_id'
_item.category_id diffrn_refln
_item.mandatory_code yes
_item_type.code code
save_
###############
# DIFFRN_SCAN #
###############
save_diffrn_scan
_category.description
; Data items in the DIFFRN_SCAN category describe the parameters of one
or more scans, relating axis positions to frames.
;
_category.id diffrn_scan
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_scan.id SCANID
_diffrn_scan.date_end ENDDATETIME
_diffrn_scan.date_start STARTDATETIME
_diffrn_scan.integration_time AVGCOUNTTIME
_diffrn_scan.frame_id_start FRAMESTARTID
_diffrn_scan.frame_id_end FRAMEENDID
_diffrn_scan.frames FRAMES
_diffrn_scan.time_period TIMEPER
_diffrn_scan.time_rstrt_incr RSTRTTIME
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/end_time=ENDDATETIME
/start_time=STARTDATETIME
/average_count_time=AVGCOUNTTIME
@units="sec"
/average_frame_time=TIMEPER
@units="sec"
/average_frame_restart_time=RSTRTTIME
@units="sec"
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/frame_start_number=FRAMESTARTNO
/frame_end_number=FRAMEENDNO
FRAMESTARTNO is the value of _diffrn_scan_frame.frame_number
for which the value of _diffrn_scan_frame.frame_id equals FRAMESTARTID
FRAMEENDNO is the value of _diffrn_scan_frame.frame_number
for which the value of _diffrn_scan_frame.frame_id equals FRAMEENDID
;
loop_
_category_key.name '_diffrn_scan.id'
'_diffrn_scan.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - derived from a suggestion by R. M. Sweet.
The vector of each axis is not given here, because it is provided in
the AXIS category. By making _diffrn_scan_axis.scan_id and
_diffrn_scan_axis.axis_id keys of the DIFFRN_SCAN_AXIS category,
an arbitrary number of scanning and fixed axes can be specified for a
scan. In this example, three rotation axes and one translation axis
at nonzero values are specified, with one axis stepping. There is no
reason why more axes could not have been specified to step. Range
information has been specified, but note that it can be calculated from
the number of frames and the increment, so the data item
_diffrn_scan_axis.angle_range could be dropped.
Both the sweep data and the data for a single frame are specified.
Note that the information on how the axes are stepped is given twice,
once in terms of the overall averages in the value of
_diffrn_scan.integration_time and the values for DIFFRN_SCAN_AXIS,
and precisely for the given frame in the value for
_diffrn_scan_frame.integration_time and the values for
DIFFRN_SCAN_FRAME_AXIS. If dose-related adjustments are made to
scan times and nonlinear stepping is done, these values may differ.
Therefore, in interpreting the data for a particular frame it is
important to use the frame-specific data.
;
;
_diffrn_scan.id 1
_diffrn_scan.date_start '2001-11-18T03:26:42'
_diffrn_scan.date_end '2001-11-18T03:36:45'
_diffrn_scan.integration_time 3.0
_diffrn_scan.frame_id_start mad_L2_000
_diffrn_scan.frame_id_end mad_L2_200
_diffrn_scan.frames 201
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
1 omega 200.0 20.0 0.1 . . .
1 kappa -40.0 0.0 0.0 . . .
1 phi 127.5 0.0 0.0 . . .
1 tranz . . . 2.3 0.0 0.0
_diffrn_scan_frame.scan_id 1
_diffrn_scan_frame.date '2001-11-18T03:27:33'
_diffrn_scan_frame.integration_time 3.0
_diffrn_scan_frame.frame_id mad_L2_018
_diffrn_scan_frame.frame_number 18
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.angle_increment
_diffrn_scan_frame_axis.displacement
_diffrn_scan_frame_axis.displacement_increment
mad_L2_018 omega 201.8 0.1 . .
mad_L2_018 kappa -40.0 0.0 . .
mad_L2_018 phi 127.5 0.0 . .
mad_L2_018 tranz . . 2.3 0.0
;
; Example 2 - a more extensive example (R. M. Sweet, P. J. Ellis &
H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the goniometer.
This leads to a choice: either the axes of
the detector are defined at the origin, and then a Z setting of -240
is entered, or the axes are defined with the necessary Z offset.
In this case, the setting is used and the offset is left as zero.
This axis is called DETECTOR_Z.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in terms of
2300 0.150 mm pixels in each direction. The ELEMENT_X axis is used to
index the first array index of the data array and the ELEMENT_Y
axis is used to index the second array index. Because the pixels
are 0.150mm X 0.150mm, the centre of the first pixel is at (0.075,
0.075) in this coordinate system.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
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]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
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
ARRAY1 1 2300 1 increasing ELEMENT_X
ARRAY1 2 2300 2 increasing ELEMENT_Y
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
ELEMENT_X ELEMENT_X 0.075 0.150
ELEMENT_Y ELEMENT_Y 0.075 0.150
# category ARRAY_ELEMENT_SIZE
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
ARRAY1 2 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
; Example 3 - Example 2 revised for a spiral scan (R. M. Sweet,
P. J. Ellis & H. J. Bernstein).
A detector is placed 240 mm along the Z axis from the
goniometer, as in Example 2 above, but in this example the
image plate is scanned in a spiral pattern from the outside edge in.
The axis for positioning the detector in the Y direction depends
on the detector Z axis. This axis is called DETECTOR_Y.
The axis for positioning the detector in the X direction depends
on the detector Y axis (and therefore on the detector Z axis).
This axis is called DETECTOR_X.
This detector may be rotated around the Y axis. This rotation axis
depends on the three translation axes. It is called DETECTOR_PITCH.
A coordinate system is defined on the face of the detector in
terms of a coupled rotation axis and radial scan axis to form
a spiral scan. The rotation axis is called ELEMENT_ROT and the
radial axis is called ELEMENT_RAD. A 150 micrometre radial pitch
and a 75 micrometre 'constant velocity' angular pitch are assumed.
Indexing is carried out first on the rotation axis and the radial axis
is made to be dependent on it.
The two axes are coupled to form an axis set ELEMENT_SPIRAL.
;
; ###CBF: VERSION 1.1
data_image_1
# category DIFFRN
_diffrn.id P6MB
_diffrn.crystal_id P6MB_CRYSTAL7
# category DIFFRN_SOURCE
loop_
_diffrn_source.diffrn_id
_diffrn_source.source
_diffrn_source.type
P6MB synchrotron 'SSRL beamline 9-1'
# category DIFFRN_RADIATION
loop_
_diffrn_radiation.diffrn_id
_diffrn_radiation.wavelength_id
_diffrn_radiation.monochromator
_diffrn_radiation.polarizn_source_ratio
_diffrn_radiation.polarizn_source_norm
_diffrn_radiation.div_x_source
_diffrn_radiation.div_y_source
_diffrn_radiation.div_x_y_source
P6MB WAVELENGTH1 'Si 111' 0.8 0.0 0.08
0.01 0.00
# category DIFFRN_RADIATION_WAVELENGTH
loop_
_diffrn_radiation_wavelength.id
_diffrn_radiation_wavelength.wavelength
_diffrn_radiation_wavelength.wt
WAVELENGTH1 0.98 1.0
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
# category DIFFRN_DETECTOR_ELEMENT
loop_
_diffrn_detector_element.id
_diffrn_detector_element.detector_id
ELEMENT1 MAR345-SN26
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_MEASUREMENT
loop_
_diffrn_measurement.diffrn_id
_diffrn_measurement.id
_diffrn_measurement.number_of_axes
_diffrn_measurement.method
P6MB GONIOMETER 3 rotation
# category DIFFRN_MEASUREMENT_AXIS
loop_
_diffrn_measurement_axis.measurement_id
_diffrn_measurement_axis.axis_id
GONIOMETER GONIOMETER_PHI
GONIOMETER GONIOMETER_KAPPA
GONIOMETER GONIOMETER_OMEGA
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
# category AXIS
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]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_ROT translation detector DETECTOR_PITCH 0 0 1 0 0 0
ELEMENT_RAD translation detector ELEMENT_ROT 0 1 0 0 0 0
# category ARRAY_STRUCTURE_LIST
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
ARRAY1 1 8309900 1 increasing ELEMENT_SPIRAL
# category ARRAY_STRUCTURE_LIST_AXIS
loop_
_array_structure_list_axis.axis_set_id
_array_structure_list_axis.axis_id
_array_structure_list_axis.angle
_array_structure_list_axis.displacement
_array_structure_list_axis.angular_pitch
_array_structure_list_axis.radial_pitch
ELEMENT_SPIRAL ELEMENT_ROT 0 . 0.075 .
ELEMENT_SPIRAL ELEMENT_RAD . 172.5 . -0.150
# category ARRAY_ELEMENT_SIZE
# the actual pixels are 0.075 by 0.150 mm
# We give the coarser dimension here.
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
ARRAY1 1 150e-6
# category ARRAY_INTENSITIES
loop_
_array_intensities.array_id
_array_intensities.binary_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.gain_esd
_array_intensities.overload
_array_intensities.undefined_value
ARRAY1 1 linear 1.15 0.2 240000 0
# category ARRAY_STRUCTURE
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
ARRAY1 "signed 32-bit integer" packed little_endian
# category ARRAY_DATA
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
ARRAY1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3801324
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
Content-MD5: 07lZFvF+aOcW85IN7usl8A==
AABRAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAZBQSr1sKNBOeOe9HITdMdDUnbq7bg
...
8REo6TtBrxJ1vKqAvx9YDMD6J18Qg83OMr/tgssjMIJMXATDsZobL90AEXc4KigE
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan.id
_item_description.description
; The value of _diffrn_scan.id uniquely identifies each
scan. The identifier is used to tie together all the
information about the scan.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_scan.id' diffrn_scan yes
'_diffrn_scan_axis.scan_id' diffrn_scan_axis yes
'_diffrn_scan_frame.scan_id' diffrn_scan_frame yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_scan_axis.scan_id' '_diffrn_scan.id'
'_diffrn_scan_frame.scan_id' '_diffrn_scan.id'
save_
save__diffrn_scan.date_end
_item_description.description
; The date and time of the end of the scan. Note that this
may be an estimate generated during the scan, before the
precise time of the end of the scan is known.
;
_item.name '_diffrn_scan.date_end'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.date_start
_item_description.description
; The date and time of the start of the scan.
;
_item.name '_diffrn_scan.date_start'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan.integration_time
_item_description.description
; Approximate average time in seconds to integrate each
step of the scan. The precise time for integration
of each particular step must be provided in
_diffrn_scan_frame.integration_time, even
if all steps have the same integration time.
;
_item.name '_diffrn_scan.integration_time'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.frame_id_start
_item_description.description
; The value of this data item is the identifier of the
first frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_start'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frame_id_end
_item_description.description
; The value of this data item is the identifier of the
last frame in the scan.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan.frame_id_end'
_item.category_id diffrn_scan
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan.frames
_item_description.description
; The value of this data item is the number of frames in
the scan.
;
_item.name '_diffrn_scan.frames'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 1
1 1
save_
save__diffrn_scan.time_period
_item_description.description
; Approximate average time in seconds between the start
of each step of the scan. The precise start-to-start
time increment of each particular step may be provided in
_diffrn_scan_frame.time_period.
;
_item.name '_diffrn_scan.time_period'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.time_rstrt_incr
_item_description.description
; Approximate average time in seconds between the end
of integration of each step of the scan than the start
of integration of the next step.
In general, this will agree with
_diffrn_scan_frame.time_rstrt_incr. The
sum of the values of _diffrn_scan_frame.integration_time
and _diffrn_scan_frame.time_rstrt_incr is the
time from the start of integration of one frame and the start of
integration for the next frame and should equal the value of
_diffrn_scan_frame.time_period for this
frame. If the individual frame values vary, then the value of
_diffrn_scan.time_rstrt_incr will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.time_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan.time_rstrt_incr'
_item.category_id diffrn_scan
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan.variant
_item_description.description
; The value of _diffrn_scan.variant gives the variant
to which the given DIFFRN_SCAN row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan.variant'
_item.category_id diffrn_scan
_item.mandatory_code implicit
_item_type.code code
save_
####################
# DIFFRN_SCAN_AXIS #
####################
save_diffrn_scan_axis
_category.description
; Data items in the DIFFRN_SCAN_AXIS category describe the settings of
axes for particular scans. Unspecified axes are assumed to be at
their zero points.
;
_category.id diffrn_scan_axis
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_scan_axis.axis_id AXISID-->
_diffrn_scan_axis.angle_start ANGSTART
_diffrn_scan_axis.angle_range ANGRANGE
_diffrn_scan_axis.angle_increment ANGINC
_diffrn_scan_axis.angle_rstrt_incr ANGRSTRT
_diffrn_scan_axis.displacement_start DISPSTART
_diffrn_scan_axis.displacement_range DISPRANGE
_diffrn_scan_axis.displacement_increment DISPINC
_diffrn_scan_axis.displacement_increment DISPINC
_diffrn_scan_axis.displacement_rstrt_incr DISPRSTRT
_diffrn_scan_axis.reference_angle ANG
_diffrn_scan_axis.reference_displacement DISP
_diffrn_scan_axis.scan_id SCANID
-->
{ /CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
for AXISEQUIPMENT=="detector"}
{ /CBF_diffrn_scan__SCANID:NXentry
/sample:NXsample
for AXISEQUIPMENT=="goniometer"}
{ /CBF_diffrn_scan__SCANID:NXentry
/coordinate_system:NXcoordinate_system
for AXISEQUIPMENT=="general"}
/transformations:NXtransformations
/AXISID=[]
@diffrn_scan_axis__angle_start=ANGSTART
@diffrn_scan_axis__angle_range=ANGRANGE
@diffrn_scan_axis__angle_increment=ANGINC
@diffrn_scan_axis__angle_rstrt_incr=ANGRSTRT
@diffrn_scan_axis__displacement_start=DISPSTART
@diffrn_scan_axis__displacement_range=DISPRANGE
@diffrn_scan_axis__displacement_increment=DISPINC
@diffrn_scan_axis__displacement_rstrt_incr=DISPRSTRT
@diffrn_scan_axis__reference_angle=ANG
@diffrn_scan_axis__reference_displacement=DISP
;
loop_
_category_key.name
'_diffrn_scan_axis.scan_id'
'_diffrn_scan_axis.axis_id'
'_diffrn_scan_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_axis.scan_id
_item_description.description
; The value of this data item is the identifier of the
scan for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_axis.scan_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the scan for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan.id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_axis.axis_id'
_item.category_id diffrn_scan_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_axis.angle_start
_item_description.description
; The starting position for the specified axis in degrees.
;
_item.name '_diffrn_scan_axis.angle_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_range
_item_description.description
; The range from the starting position for the specified axis
in degrees.
;
_item.name '_diffrn_scan_axis.angle_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_increment
_item_description.description
; The increment for each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_increment. The
sum of the values of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.angle_rstrt_incr
_item_description.description
; The increment after each step for the specified axis
in degrees. In general, this will agree with
_diffrn_scan_frame_axis.angle_rstrt_incr. The
sum of the values of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment
and _diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.angle for this
next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.angle_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.angle_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.displacement_start
_item_description.description
; The starting position for the specified axis in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_start'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_range
_item_description.description
; The range from the starting position for the specified axis
in millimetres.
;
_item.name '_diffrn_scan_axis.displacement_range'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_increment
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_increment.
The sum of the values of
_diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for a given frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_increment will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_increment (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_increment'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.displacement_rstrt_incr
_item_description.description
; The increment for each step for the specified axis
in millimetres. In general, this will agree with
_diffrn_scan_frame_axis.displacement_rstrt_incr.
The sum of the values of
_diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame relative to a given frame and
should equal _diffrn_scan_frame_axis.displacement
for this next frame. If the individual frame values
vary, then the value of
_diffrn_scan_axis.displacement_rstrt_incr will be
representative
of the ensemble of values of
_diffrn_scan_frame_axis.displacement_rstrt_incr (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_angle.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_angle will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_angle (e.g.
the mean).
If not specified, the value defaults to zero.
;
_item.name '_diffrn_scan_axis.reference_angle'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres
against which measurements of the reference beam center
and reference detector distance should be made.
In general, this will agree with
_diffrn_scan_frame_axis.reference_displacement.
If the individual frame values vary, then the value of
_diffrn_scan_axis.reference_displacement will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.reference_displacement (e.g.
the mean).
;
_item.name '_diffrn_scan_axis.reference_displacement'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_axis.variant
_item_description.description
; The value of _diffrn_scan_axis.variant gives the variant
to which the given DIFFRN_SCAN_AXIS row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_axis.variant'
_item.category_id diffrn_scan_axis
_item.mandatory_code implicit
_item_type.code code
save_
#####################
# DIFFRN_SCAN_FRAME #
#####################
save_diffrn_scan_frame
_category.description
; Data items in the DIFFRN_SCAN_FRAME category describe
the relationships of particular frames to scans.
;
_category.id diffrn_scan_frame
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_scan_frame.date DATETIME
_diffrn_scan_frame.frame_id ID
_diffrn_scan_frame.frame_number FRAMENUMBER
_diffrn_scan_frame.integration_time COUNTTIME
_diffrn_scan_frame.polarizn_Stokes_I STOKESI
_diffrn_scan_frame.polarizn_Stokes_Q STOKESQ
_diffrn_scan_frame.polarizn_Stokes_U STOKESU
_diffrn_scan_frame.polarizn_Stokes_V STOKESV
_diffrn_scan_frame.scan_id SCANID
_diffrn_scan_frame.time_period FRAMETIME
_diffrn_scan_frame.time_rstrt_incr RSTRTTIME
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
/CBF_diffrn_scan_frame__date=["DATETIME"]
/CBF_diffrn_scan_frame__frame_id=["ID"]
/count_time=[COUNTIME]
/frame_time=[FRAMETIME]
/frame_restart_time=[RSTRTTIME]
/sample:NXsample
/beam:NXbeam
/incident_polarisation_stokes=[STOKESI,STOKESQ,STOKESU,STOKESV]
@units="Watts/meter^2"
where each array element is inserted at index FRAMENUMBER
;
loop_
_category_key.name
'_diffrn_scan_frame.scan_id'
'_diffrn_scan_frame.frame_id'
'_diffrn_scan_frame.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame.date
_item_description.description
; The date and time of the start of the frame being scanned.
;
_item.name '_diffrn_scan_frame.date'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__diffrn_scan_frame.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame being examined.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame.frame_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.frame_number
_item_description.description
; The value of this data item is the number of the frame
within the scan, starting with 1. It is not necessarily
the same as the value of _diffrn_scan_frame.frame_id,
but it may be.
;
_item.name '_diffrn_scan_frame.frame_number'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
. 0
0 0
save_
save__diffrn_scan_frame.integration_time
_item_description.description
; The time in seconds to integrate this step of the scan.
This should be the precise time of integration of each
particular frame. The value of this data item should
be given explicitly for each frame and not inferred
from the value of _diffrn_scan.integration_time.
;
_item.name '_diffrn_scan_frame.integration_time'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.polarizn_Stokes_I
_item_description.description
;
Ip+In+Inp, where where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization,
In is the intensity (amplitude squared) of the electric vector
in the plane of the normal to the plane of polarization,
and Inp is the intensity (amplitude squared) of the non-
polarized (incoherent) electric vector.
This is an average or other representative sample of the
frame.
This is the first of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
Note that, if the polarized intensity Ip+In is required,
(Ip+In)^2 is the sum of Q^2+U^2+V^2.
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_I'
_item.category_id diffrn_scan_frame
_item.mandatory_code implicit
_item_default.value 1.0
loop_
_item_range.maximum
_item_range.minimum
. 0.0
0.0 0.0
_item_type.code float
save_
save__diffrn_scan_frame.polarizn_Stokes_I_esd
_item_description.description
; The setimated standard deviation of
_diffrn_scan_frame.polarizn_Stokes_I,
Ip+In+Inp, where where Ip is the intensity (amplitude squared)
of the electric vector in the plane of polarization,
In is the intensity (amplitude squared) of the electric vector
in the plane of the normal to the plane of polarization,
and Inp is the intensity (amplitude squared) of the non-
polarized (incoherent) electric vector.
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_I_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_scan_frame.polarizn_Stokes_I'
'associated_value'
save_
save__diffrn_scan_frame.polarizn_Stokes_Q
_item_description.description
;
(Ip-In)*cos(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
This is an average or other representative sample of the
frame.
This is the second of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_Q'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
loop_
_item_type.code float
save_
save__diffrn_scan_frame.polarizn_Stokes_Q_esd
_item_description.description
; The setimated standard deviation of
_diffrn_scan_frame.polarizn_Stokes_Q,
(Ip-In)*cos(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_Q_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_scan_frame.polarizn_Stokes_Q'
'associated_value'
save_
save__diffrn_scan_frame.polarizn_Stokes_U
_item_description.description
;
(Ip-In)*sin(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
This is an average or other representative sample of the
frame.
This is the third of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_U'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
loop_
_item_type.code float
save_
save__diffrn_scan_frame.polarizn_Stokes_U_esd
_item_description.description
; The setimated standard deviation of
_diffrn_scan_frame.polarizn_Stokes_U,
(Ip-In)*sin(2*theta), where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization, In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_U_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_scan_frame.polarizn_Stokes_U'
'associated_value'
save_
save__diffrn_scan_frame.polarizn_Stokes_V
_item_description.description
;
+/-2*sqrt(IpIn), with a + sign for right-handed circular
polarization, where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
This is an average or other representative sample of the
frame.
This is the fourth of the Stokes polarization parameters,
I, Q, U, V (also known as I, M, C, S). See
H. H. Berry, G. Gabrielse, A. E. Livingston (1977),
"Measurement of the Stokes parameters of Light",
Applied Optics, 16:12, 3200 -- 3205.
If the absolute intensity is not known, the value 1.
is assumed for I, and all 4 Stokes parameters are
dimensionless. When the absolute intensity is known,
all 4 Stokes parameters are in units of Watts per
square meter.
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_V'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
loop_
_item_type.code float
save_
save__diffrn_scan_frame.polarizn_Stokes_V_esd
_item_description.description
; The setimated standard deviation of
_diffrn_scan_frame.polarizn_Stokes_V,
+/-2*sqrt(IpIn), with a + sign for right-handed circular
polarization, where where Ip is the intensity
(amplitude squared) of the electric vector in the plane of
polarization and In is the intensity (amplitude squared) of
the electric vector in the plane of the normal to the
plane of polarization, and theta is the angle as viewed
from the specimen, between the normal to the polarization
plane and the laboratory Y axis as defined in the
AXIS category.
;
_item.name '_diffrn_scan_frame.polarizn_Stokes_V_esd'
_item.category_id diffrn_radiation
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
loop_
_item_related.related_name
_item_related.function_code '_diffrn_scan_frame.polarizn_Stokes_V'
'associated_value'
save_
save__diffrn_scan_frame.scan_id
_item_description.description
; The value of _diffrn_scan_frame.scan_id identifies the scan
containing this frame.
This item is a pointer to _diffrn_scan.id in the
DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame.scan_id'
_item.category_id diffrn_scan_frame
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame.time_period
_item_description.description
; The time in seconds between the start of this frame and the
start of the next frame, if any. If there is no next frame,
a null value should be given.
;
_item.name '_diffrn_scan_frame.time_period'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.time_rstrt_incr
_item_description.description
; The time in seconds between the end of integration of this step of the scan
and the start of integration of the next step.
The sum of the values of _diffrn_scan_frame.integration_time
and _diffrn_scan_frame.time_rstrt_incr is the
time from the start of integration of one frame and the start of
integration for the next frame and should equal the value of
_diffrn_scan_frame.time_period for this
frame. The value of _diffrn_scan.time_rstrt_incr will be
representative of the ensemble of values of
_diffrn_scan_frame_axis.time_rstrt_incr (e.g.
the mean).
If there is no next frame, a null value should be given.
;
_item.name '_diffrn_scan_frame.time_rstrt_incr'
_item.category_id diffrn_scan_frame
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame.variant
_item_description.description
; The value of _diffrn_scan_frame.variant gives the variant
to which the given DIFFRN_SCAN_FRAME row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame.variant'
_item.category_id diffrn_scan_frame
_item.mandatory_code implicit
_item_type.code code
save_
##########################
# DIFFRN_SCAN_FRAME_AXIS #
##########################
save_diffrn_scan_frame_axis
_category.description
; Data items in the DIFFRN_SCAN_FRAME_AXIS category describe the
settings of axes for particular frames. Unspecified axes are
assumed to be at their zero points. If, for any given frame,
nonzero values apply for any of the data items in this category,
those values should be given explicitly in this category and not
simply inferred from values in DIFFRN_SCAN_AXIS.
;
_category.id diffrn_scan_frame_axis
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_scan_frame_axis.axis_id AXISID
_diffrn_scan_frame_axis.angle ANGLE
_diffrn_scan_frame_axis.angle_increment ANGLEINCREMENT
_diffrn_scan_frame_axis.angle_rstrt_incr ANGLERSTRTINCREMENT
_diffrn_scan_frame_axis.displacement DISP
_diffrn_scan_frame_axis.displacement_increment DISPINCREMENT
_diffrn_scan_frame_axis.displacement_rstrt_incr DISPRSTRTINCREMENT
_diffrn_scan_frame_axis.reference_angle REFANGLE
_diffrn_scan_frame_axis.reference_displacement REFDISP
{ /CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/instrument:NXinstrument
/CBF_diffrn_detector__DETECTORNAME:NXdetector
for AXISEQUIPMENT=="detector"}
{ /CBF_diffrn_scan__SCANID:NXentry
/sample:NXsample
for AXISEQUIPMENT=="goniometer"}
{ /CBF_diffrn_scan__SCANID:NXentry
/coordinate_system:NXcoordinate_system
for AXISEQUIPMENT=="general"}
/transformations:NXtransformations
/AXISID=[]
@diffrn_scan_frame_axis__angle_start=[ANGSTART]
@diffrn_scan_frame_axis__angle_range=[ANGRANGE]
@diffrn_scan_frame_axis__angle_increment=[ANGINC]
@diffrn_scan_frame_axis__angle_rstrt_incr=[ANGRSTRT]
@diffrn_scan_frame_axis__displacement_start=[DISPSTART]
@diffrn_scan_frame_axis__displacement_range=[DISPRANGE]
@diffrn_scan_frame_axis__displacement_increment=[DISPINC]
@diffrn_scan_frame_axis__displacement_rstrt_incr=[DISPRSTRT]
@diffrn_scan_frame_axis__reference_angle=[ANG]
@diffrn_scan_frame_axis__reference_displacement=[DISP]
note that @units="mm" or @units="deg" should also be specified.
The dimensions of the array depend on np (the number of frames = the
value of _diffrn_scan.frames)
either DISP OR ANGLE is inserted as the i-th element
counting from 1 in AXISID where i is the value of
_diffrn_scan_frame.frame_number for which the value
of _diffrn_scan_frame.frame_id agrees with the
value of _diffrn_scan_frame_axis.frame_id
The remaining tags similarly populate the attribute arrays
;
loop_
_category_key.name
'_diffrn_scan_frame_axis.frame_id'
'_diffrn_scan_frame_axis.axis_id'
'_diffrn_scan_frame_axis.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
save_
save__diffrn_scan_frame_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes for the frame for which settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_diffrn_scan_frame_axis.axis_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.angle
_item_description.description
; The setting of the specified axis in degrees for this frame.
This is the setting at the start of the integration time.
;
_item.name '_diffrn_scan_frame_axis.angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_increment
_item_description.description
; The increment for this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle and
_diffrn_scan_frame_axis.angle_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.angle_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.angle_rstrt_incr
_item_description.description
; The increment after this frame for the angular setting of
the specified axis in degrees. The sum of the values
of _diffrn_scan_frame_axis.angle,
_diffrn_scan_frame_axis.angle_increment and
_diffrn_scan_frame_axis.angle_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.angle for this next frame.
;
_item.name '_diffrn_scan_frame_axis.angle_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame. This is the setting at the start of the integration
time.
;
_item.name '_diffrn_scan_frame_axis.displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_increment
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement and
_diffrn_scan_frame_axis.displacement_increment is the
angular setting of the axis at the end of the integration
time for this frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_increment'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.displacement_rstrt_incr
_item_description.description
; The increment for this frame for the displacement setting of
the specified axis in millimetres. The sum of the values
of _diffrn_scan_frame_axis.displacement,
_diffrn_scan_frame_axis.displacement_increment and
_diffrn_scan_frame_axis.displacement_rstrt_incr is the
angular setting of the axis at the start of the integration
time for the next frame and should equal
_diffrn_scan_frame_axis.displacement for this next frame.
;
_item.name '_diffrn_scan_frame_axis.displacement_rstrt_incr'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.frame_id
_item_description.description
; The value of this data item is the identifier of the
frame for which axis settings are being specified.
Multiple axes may be specified for the same value of
_diffrn_scan_frame.frame_id.
This item is a pointer to _diffrn_data_frame.id in the
DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_axis.frame_id'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_axis.reference_angle
_item_description.description
; The setting of the specified axis in degrees
against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be zero.
;
_item.name '_diffrn_scan_frame_axis.reference_angle'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__diffrn_scan_frame_axis.reference_displacement
_item_description.description
; The setting of the specified axis in millimetres for this
frame against which measurements of the reference beam center
and reference detector distance should be made.
This is normally the same for all frames, but the
option is provided here of making changes when
needed.
If not provided, it is assumed to be equal to
_diffrn_scan_frame_axis.displacement.
;
_item.name '_diffrn_scan_frame_axis.reference_displacement'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
save__diffrn_scan_frame_axis.variant
_item_description.description
; The value of _diffrn_scan_frame_axis.variant gives the variant
to which the given DIFFRN_SCAN_FRAME_AXIS row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame_axis.variant'
_item.category_id diffrn_scan_frame_axis
_item.mandatory_code implicit
_item_type.code code
save_
#############################
# DIFFRN_SCAN_FRAME_MONITOR #
#############################
save_diffrn_scan_frame_monitor
_category.description
; Data items in the DIFFRN_SCAN_FRAME_MONITOR category record
the values and details about each monitor for each frame of data
during a scan.
Each monitor value is uniquely identified by the combination of
the scan_id given by _diffrn_scan_frame.scan_id
the frame_id given by _diffrn_scan_frame_monitor.frame_id,
the monitor's detector_id given by
_diffrn_scan_frame_monitor.detector_id,
and a 1-based ordinal given by _diffrn_scan_frame_monitor.id.
If there is only one frame for the scan, the value of
_diffrn_scan_frame_monitor.frame_id may be
omitted.
A single frame may have more than one monitor value, and each
monitor value may be the result of integration over the entire
frame integration time given by the value of
_diffrn_scan_frame.integration_time
or many monitor values may be reported over shorter times given
by the value of _diffrn_scan_frame_monitor.integration_time. If
only one monitor value for a given monitor is collected during
the integration time of the frame, the value of
_diffrn_scan_frame_monitor.id may be
omitted.
;
_category.id diffrn_scan_frame_monitor
_category.mandatory_code no
_category.NX_mapping_details
;
_diffrn_scan_frame_monitor.id MONID -->
_diffrn_scan_frame_monitor.detector_id DETECTORNAME -->
_diffrn_scan_frame_monitor.scan_id SCANID -->
_diffrn_scan_frame_monitor.frame_id FRAMEID -->
_diffrn_scan_frame_monitor.integration_time INTEGRATIONTIME -->
_diffrn_scan_frame_monitor.monitor_value MONITORVALUE -->
-->
/CBF_diffrn_scan__SCANID:NXentry
/CBF_scan_id="SCANID"
/instrument:NXinstrument
/CBF_diffrn_scan_frame_monitor__DETECTORNAME_MONID:NXmonitor
@CBF_detector_id="DETECTORNAME"
@CBF_diffrn_scan_frame_monitor__id="MONID"
/data=[MONITORVALUE]
/count_time=[INTEGRATIONTIME]
;
loop_
_category_key.name '_diffrn_scan_frame_monitor.id'
'_diffrn_scan_frame_monitor.detector_id'
'_diffrn_scan_frame_monitor.scan_id'
'_diffrn_scan_frame_monitor.frame_id'
'_diffrn_scan_frame_monitor.variant'
loop_
_category_group.id 'inclusive_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - The beam intensity for frame FRAME1 is being tracked
by a beamstop monitor detector BSM01, made from metal foil and
a PIN diode, locate 20 mm in front of a MAR345 detector and being
sampled every 2 seconds in a 20 second scan.
;
;
# category DIFFRN_DETECTOR
loop_
_diffrn_detector.diffrn_id
_diffrn_detector.id
_diffrn_detector.type
_diffrn_detector.number_of_axes
P6MB MAR345-SN26 'MAR 345' 4
P6MB BSM01 'metal foil and PIN diode' 1
# category DIFFRN_DETECTOR_AXIS
loop_
_diffrn_detector_axis.detector_id
_diffrn_detector_axis.axis_id
MAR345-SN26 DETECTOR_X
MAR345-SN26 DETECTOR_Y
MAR345-SN26 DETECTOR_Z
MAR345-SN26 DETECTOR_PITCH
BSM01 MONITOR_Z
# category DIFFRN_DATA_FRAME
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
FRAME1 ELEMENT1 ARRAY1 1
# category DIFFRN_SCAN
loop_
_diffrn_scan.id
_diffrn_scan.frame_id_start
_diffrn_scan.frame_id_end
_diffrn_scan.frames
SCAN1 FRAME1 FRAME1 1
# category DIFFRN_SCAN_AXIS
loop_
_diffrn_scan_axis.scan_id
_diffrn_scan_axis.axis_id
_diffrn_scan_axis.angle_start
_diffrn_scan_axis.angle_range
_diffrn_scan_axis.angle_increment
_diffrn_scan_axis.displacement_start
_diffrn_scan_axis.displacement_range
_diffrn_scan_axis.displacement_increment
SCAN1 GONIOMETER_OMEGA 12.0 1.0 1.0 0.0 0.0 0.0
SCAN1 GONIOMETER_KAPPA 23.3 0.0 0.0 0.0 0.0 0.0
SCAN1 GONIOMETER_PHI -165.8 0.0 0.0 0.0 0.0 0.0
SCAN1 DETECTOR_Z 0.0 0.0 0.0 -240.0 0.0 0.0
SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.6 0.0 0.0
SCAN1 DETECTOR_X 0.0 0.0 0.0 -0.5 0.0 0.0
SCAN1 DETECTOR_PITCH 0.0 0.0 0.0 0.0 0.0 0.0
SCAN1 MONITOR_Z 0.0 0.0 0.0 -220.0 0.0 0.0
# category DIFFRN_SCAN_FRAME
loop_
_diffrn_scan_frame.frame_id
_diffrn_scan_frame.frame_number
_diffrn_scan_frame.integration_time
_diffrn_scan_frame.scan_id
_diffrn_scan_frame.date
FRAME1 1 20.0 SCAN1 1997-12-04T10:23:48
# category DIFFRN_SCAN_FRAME_MONITOR
loop_
_diffrn_scan_frame_monitor.id
_diffrn_scan_frame_monitor.detector_id
_diffrn_scan_frame_monitor.scan_id
_diffrn_scan_frame_monitor.frame_id
_diffrn_scan_frame_monitor.integration_time
_diffrn_scan_frame_monitor.monitor_value
1 BSM01 SCAN1 FRAME1 2.0 23838345642
2 BSM01 SCAN1 FRAME1 2.0 23843170669
3 BSM01 SCAN1 FRAME1 2.0 23839478690
4 BSM01 SCAN1 FRAME1 2.0 23856642085
5 BSM01 SCAN1 FRAME1 2.0 23781717656
6 BSM01 SCAN1 FRAME1 2.0 23788850775
7 BSM01 SCAN1 FRAME1 2.0 23815576677
8 BSM01 SCAN1 FRAME1 2.0 23789299964
9 BSM01 SCAN1 FRAME1 2.0 23830195536
10 BSM01 SCAN1 FRAME1 2.0 23673082270
# category DIFFRN_SCAN_FRAME_AXIS
loop_
_diffrn_scan_frame_axis.frame_id
_diffrn_scan_frame_axis.axis_id
_diffrn_scan_frame_axis.angle
_diffrn_scan_frame_axis.displacement
FRAME1 GONIOMETER_OMEGA 12.0 0.0
FRAME1 GONIOMETER_KAPPA 23.3 0.0
FRAME1 GONIOMETER_PHI -165.8 0.0
FRAME1 DETECTOR_Z 0.0 -240.0
FRAME1 DETECTOR_Y 0.0 0.6
FRAME1 DETECTOR_X 0.0 -0.5
FRAME1 DETECTOR_PITCH 0.0 0.0
FRAME1 MONITOR_Z 0.0 -220.0
# category AXIS
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]
GONIOMETER_OMEGA rotation goniometer . 1 0 0 . . .
GONIOMETER_KAPPA rotation goniometer GONIOMETER_OMEGA 0.64279
0 0.76604 . . .
GONIOMETER_PHI rotation goniometer GONIOMETER_KAPPA 1 0 0
. . .
SOURCE general source . 0 0 1 . . .
GRAVITY general gravity . 0 -1 0 . . .
DETECTOR_Z translation detector . 0 0 1 0 0 0
DETECTOR_Y translation detector DETECTOR_Z 0 1 0 0 0 0
DETECTOR_X translation detector DETECTOR_Y 1 0 0 0 0 0
DETECTOR_PITCH rotation detector DETECTOR_X 0 1 0 0 0 0
ELEMENT_X translation detector DETECTOR_PITCH
1 0 0 172.43 -172.43 0
ELEMENT_Y translation detector ELEMENT_X
0 1 0 0 0 0
MONITOR_Z translation detector . 0 0 1 0 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_scan_frame_monitor.id
_item_description.description
; This item is an integer identifier which, along with
_diffrn_scan_frame_monitor.detector_id,
_diffrn_scan_frame_monitor.scan_id, and
_diffrn_scan_frame_monitor.frame_id
should uniquely identify the monitor value being recorded
If _array_data.binary_id is not explicitly given,
it defaults to 1.
;
_item.name '_diffrn_scan_frame_monitor.id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code implicit
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__diffrn_scan_frame_monitor.detector_id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
;
_item.name '_diffrn_scan_frame_monitor.detector_id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_monitor.frame_id
_item_description.description
; This item is a pointer to _diffrn_data_frame.id
in the DIFFRN_DATA_FRAME category.
;
_item.name '_diffrn_scan_frame_monitor.frame_id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_monitor.scan_id
_item_description.description
; This item is a pointer to _diffrn_scan.id in
the DIFFRN_SCAN category.
;
_item.name '_diffrn_scan_frame_monitor.scan_id'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_scan_frame_monitor.integration_time
_item_description.description
; The precise time for integration of the monitor value given in
_diffrn_scan_frame_monitor.value
must be given in _diffrn_scan_frame_monitor.integration_time.
;
_item.name '_diffrn_scan_frame_monitor.integration_time'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code no
_item_type.code float
_item_units.code 'seconds'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame_monitor.value
_item_description.description
; The value reported by the monitor detector should be given in
_diffrn_scan_frame_monitor.value.
The value is typed as float to allow of monitors for very intense beams
that cannot report all digits, but when available, all digits of the
monitor should be recorded.
;
_item.name '_diffrn_scan_frame_monitor.value'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code no
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
save__diffrn_scan_frame_monitor.variant
_item_description.description
; The value of _diffrn_scan_frame_monitor.variant gives the variant
to which the given DIFFRN_SCAN_FRAME_MONITOR row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_diffrn_scan_frame_monitor.variant'
_item.category_id diffrn_scan_frame_monitor
_item.mandatory_code implicit
_item_type.code code
save_
#######
# MAP #
#######
save_map
_category.description
; Data items in the MAP category record
the details of a maps. Maps record values of parameters,
such as density, that are functions of position within
a cell or are functions of orthogonal coordinates in
three space.
A map may is composed of one or more map segments
specified in the MAP_SEGMENT category.
Examples are given in the MAP_SEGMENT category.
;
_category.id map
_category.mandatory_code no
loop_
_category_key.name '_map.id'
'_map.diffrn_id'
'_map.entry_id'
'_map.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'map_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.details
_item_description.description
; The value of _map.details should give a
description of special aspects of each map.
;
_item.name '_map.details'
_item.category_id map
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
DIFFRN category.
;
_item.name '_map.diffrn_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
ENTRY category.
;
_item.name '_map.entry_id'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
save__map.id
_item_description.description
; The value of _map.id must uniquely identify
each map for the given diffrn.id or entry.id.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map.id' map yes
'_map_segment.id' map_segment yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_map_segment.id' '_map.id'
save_
save__map.variant
_item_description.description
; The value of _map.variant gives the variant
to which the given map row is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_map.variant'
_item.category_id map
_item.mandatory_code implicit
_item_type.code code
save_
###############
# MAP_SEGMENT #
###############
save_map_segment
_category.description
; Data items in the MAP_SEGMENT category record
the details about each segment (section or brick) of a map.
;
_category.id map_segment
_category.mandatory_code no
loop_
_category_key.name '_map_segment.id'
'_map_segment.map_id'
'_map_segment.variant'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
'map_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Identifying an observed density map
and a calculated density map, each consisting of one
segment, both using the same array structure
and mask.
;
;
loop_
_map.id
_map.details
rho_calc
;
density calculated from F_calc derived from the ATOM_SITE list
;
rho_obs
;
density combining the observed structure factors with the
calculated phases
;
loop_
_map_segment.map_id
_map_segment.id
_map_segment.array_id
_map_segment.binary_id
_map_segment.mask_array_id
_map_segment.mask_binary_id
rho_calc rho_calc map_structure 1 mask_structure 1
rho_obs rho_obs map_structure 2 mask_structure 1
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__map_segment.array_id
_item_description.description
; The value of _map_segment.array_id identifies the array
structure into which the map is organized.
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.array_section_id
_item_description.description
; This item is a pointer to _array_structure_list_section.id
in the a href="#array_structure_list_section">"ARRAY_STRUCTURE_LIST_SECTION category.
;
_item.name '_map_segment.array_section_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.binary_id
_item_description.description
; The value of _map_segment.binary_id distinguishes the particular
set of data organized according to _map_segment.array_id in
which the data values of the map are stored.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.mask_array_id
_item_description.description
; The value of _map_segment.mask_array_id, if given, the array
structure into which the mask for the map is organized. If no
value is given, then all elements of the map are valid. If a
value is given, then only elements of the map for which the
corresponding element of the mask is non-zero are valid. The
value of _map_segment.mask_array_id differs from the value of
_map_segment.array_id in order to permit the mask to be given
as, say, unsigned 8-bit integers, while the map is given as
a data type with more range. However, the two array structures
must be aligned, using the same axes in the same order with the
same displacements and increments
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_map_segment.mask_array_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
save__map_segment.mask_binary_id
_item_description.description
; The value of _map_segment.mask_binary_id identifies the
particular set of data organized according to
_map_segment.mask_array_id specifying the mask for the map.
This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_map_segment.mask_binary_id'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code int
save_
save__map_segment.id
_item_description.description
; The value of _map_segment.id must uniquely
identify each segment of a map.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_map_segment.id'
map_segment
yes
_item_type.code code
save_
save__map_segment.map_id
_item_description.description
; This item is a pointer to _map.id
in the MAP category.
;
_item.name '_map_segment.map_id'
_item.category_id map_segment
_item.mandatory_code yes
_item_type.code code
save_
save__map_segment.details
_item_description.description
; The value of _map_segment.details should give a
description of special aspects of each segment of a map.
;
_item.name '_map_segment.details'
_item.category_id map_segment
_item.mandatory_code no
_item_type.code text
loop_
_item_examples.case
_item_examples.detail
; Example to be provided
;
;
;
save_
save__map_segment.variant
_item_description.description
; The value of _map_segment.variant gives the variant
to which the given map segment is related.
If this value is not given, the variant is assumed to the default
null variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_map_segment.variant'
_item.category_id map_segment
_item.mandatory_code implicit
_item_type.code code
save_
###########
# VARIANT #
###########
save_variant
_category.description
; Data items in the VARIANT category record
the details about sets of variants of data items.
There is sometimes a need to allow for multiple versions of the
same data items in order to allow for refinements and corrections
to earlier assumptions, observations and calculations. In order
to allow data sets to contain more than one variant of the same
information, an optional ...variant data item as a pointer to
_variant.variant has been added to the key of every category,
as an implicit data item with a null (empty) default value.
All rows in a category with the same variant value are considered
to be related to one another and to all rows in other categories
with the same variant value. For a given variant, all such rows
are also considered to be related to all rows with a null variant
value, except that a row with a null variant value is for which
all other components of its key are identical to those entries
in another row with a non-null variant value is not related the
the rows with that non-null variant value. This behavior is
similar to the convention for identifying alternate conformers
in an atom list.
An optional role may be specified for a variant as the value of
_variant.role. Possible roles are null, "preferred",
"raw data", "unsuccessful trial".
variants may carry an optional timestamp as the value of
_variant.timestamp.
variants may be related to other variants from which they were
derived by the value of _variant.variant_of
Further details about the variant may be specified as the value
of _variant.details.
In order to allow variant information from multiple datasets to
be combined, _variant.diffrn_id and/or _variant.entry_id may
be used.
;
_category.id variant
_category.mandatory_code no
loop_
_category_key.name '_variant.variant'
'_variant.diffrn_id'
'_variant.entry_id'
loop_
_category_group.id 'inclusive_group'
'variant_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - Distinguishing between a raw beam center and a refined beam
center inferred after indexing. Detector d1 is composed of
four CCD detector elements, each 200 mm by 200 mm, arranged
in a square, in the pattern
1 2
*
3 4
Note that the beam centre is slightly displaced from each of the
detector elements, just beyond the lower right corner of 1,
the lower left corner of 2, the upper right corner of 3 and
the upper left corner of 4. For each element, the detector
face coordiate system, is assumed to have the fast axis
running from left to right and the slow axis running from
top to bottom with the origin at the top left corner.
After indexing and refinement, the center is shifted by .2 mm
left and .1 mm down.
;
;
loop_
_variant.variant
_variant.role
_variant.timestamp
_variant.variant_of
_variant.details
. "raw data" 2007-08-03T23:20:00 . .
indexed "preferred" 2007-08-04T01:17:28 .
"indexed cell and refined beam center"
loop_
_diffrn_detector_element.detector_id
_diffrn_detector_element.id
_diffrn_detector_element.reference_center_fast
_diffrn_detector_element.reference_center_slow
_diffrn_detector_element.reference_center_units
_diffrn_detector_element.variant
d1 d1_ccd_1 201.5 201.5 mm .
d1 d1_ccd_2 -1.8 201.5 mm .
d1 d1_ccd_3 201.6 -1.4 mm .
d1 d1_ccd_4 -1.7 -1.5 mm .
d1 d1_ccd_1 201.3 201.6 mm indexed
d1 d1_ccd_2 -2.0 201.6 mm indexed
d1 d1_ccd_3 201.3 -1.5 mm indexed
d1 d1_ccd_4 -1.9 -1.6 mm indexed
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__variant.details
_item_description.description
; A description of special aspects of the variant.
;
_item.name '_variant.details'
_item.category_id variant
_item.mandatory_code no
_item_type.code text
_item_examples.case
; indexed cell and refined beam center
;
save_
save__variant.diffrn_id
_item_description.description
; This item is a pointer to _diffrn.id in the
diffrn category.
;
_item.name '_variant.diffrn_id'
_item.category_id variant
_item.mandatory_code implicit
_item_type.code code
save_
save__variant.entry_id
_item_description.description
; This item is a pointer to _entry.id in the
entry category
;
_item.name '_variant.entry_id'
_item.category_id variant
_item.mandatory_code yes
_item_type.code code
save_
save__variant.role
_item_description.description
; The value of _variant.role specified a role
for this variant. Possible roles are null, "preferred",
"raw data", and "unsuccessful trial".
A null value for _variant.role leaves the
precise role of the variant unspecified. No inference should
be made that the variant with the latest time stamp is
preferred.
;
_item.name '_variant.role'
_item.category_id variant
_item.mandatory_code no
_item_type.code uline
loop_
_item_enumeration.value
_item_enumeration.detail
"preferred"
; A value of "preferred" indicates that rows of any categories specifying
this variant should be used in preference to rows with the same key
specifying other variants or the null variant. It is an error to specify
two variants that appear in the same category with the same key as being
preferred, but it is not an error to specify more than one variant as
preferred in other cases.
;
"raw data"
; A value of "raw data" indicates data prior to any corrections,
calculations or refinements. It is not necessarily an error for raw data
to also be a variant of an earlier variant. It may be replacement raw
data for earlier data believed to be erroneous.
;
"unsuccessful trial"
; A value of "unsuccessful trial" indicates data that should not be used
for further calculation.
;
save_
save__variant.timestamp
_item_description.description
; The date and time identifying a variant. This is not
necessarily the precise time of the measurement or calculation
of the individual related data items, but a timestamp that
reflects the order in which the variants were defined.
;
_item.name '_variant.timestamp'
_item.category_id variant
_item.mandatory_code no
_item_type.code yyyy-mm-dd
save_
save__variant.variant
_item_description.description
; The value of _variant.variant must uniquely identify
each variant for the given diffraction experiment and/or entry
This item has been made implicit and given a default value of
null.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_variant.variant' variant implicit
'_variant.variant_of' variant implicit
'_array_data.variant' array_data implicit
'_array_element_size.variant' array_element_size implicit
'_array_intensities.variant' array_intensities implicit
'_array_structure.variant' array_structure implicit
'_array_structure_list.variant' array_structure_list
implicit
'_array_structure_list_axis.variant' array_structure_list_axis
implicit
'_array_structure_list_section.variant' array_structure_list_axis_section
implicit
'_axis.variant' axis implicit
'_diffrn_data_frame.variant' diffrn_data_frame implicit
'_diffrn_detector.variant' diffrn_detector implicit
'_diffrn_detector_axis.variant' diffrn_detector_axis
implicit
'_diffrn_detector_element.variant' diffrn_detector_element
implicit
'_diffrn_measurement.variant' diffrn_measurement implicit
'_diffrn_measurement_axis.variant' diffrn_measurement_axis
implicit
'_diffrn_radiation.variant' diffrn_radiation implicit
'_diffrn_refln.variant' diffrn_refln implicit
'_diffrn_scan.variant' diffrn_scan implicit
'_diffrn_scan_axis.variant' diffrn_scan_axis implicit
'_diffrn_scan_frame.variant' diffrn_scan_frame implicit
'_diffrn_scan_frame_axis.variant' diffrn_scan_frame_axis
implicit
'_diffrn_scan_frame_monitor.variant' diffrn_scan_frame_monitor
implicit
'_map.variant' map implicit
'_map_segment.variant' map_segment implicit
_item_default.value .
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.variant' '_variant.variant'
'_array_element_size.variant' '_variant.variant'
'_array_intensities.variant' '_variant.variant'
'_array_structure.variant' '_variant.variant'
'_array_structure_list.variant' '_variant.variant'
'_array_structure_list_axis.variant' '_variant.variant'
'_axis.variant' '_variant.variant'
'_diffrn_data_frame.variant' '_variant.variant'
'_diffrn_detector.variant' '_variant.variant'
'_diffrn_detector_axis.variant' '_variant.variant'
'_diffrn_detector_element.variant' '_variant.variant'
'_diffrn_measurement.variant' '_variant.variant'
'_diffrn_measurement_axis.variant' '_variant.variant'
'_diffrn_radiation.variant' '_variant.variant'
'_diffrn_refln.variant' '_variant.variant'
'_diffrn_scan.variant' '_variant.variant'
'_diffrn_scan_axis.variant' '_variant.variant'
'_diffrn_scan_frame.variant' '_variant.variant'
'_diffrn_scan_frame_axis.variant' '_variant.variant'
'_diffrn_scan_frame_monitor.variant' '_variant.variant'
'_map.variant' '_variant.variant'
'_map_segment.variant' '_variant.variant'
save_
save__variant.variant_of
_item_description.description
; The value of _variant.variant_of gives the variant
from which this variant was derived. If this value is not given,
the variant is assumed to be derived from the default null
variant.
This item is a pointer to _variant.variant in the
VARIANT category.
;
_item.name '_variant.variant_of'
_item.category_id variant
_item.mandatory_code no
_item_type.code code
save_
######################## DEPRECATED DATA ITEMS ########################
save__diffrn_detector_axis.id
_item_description.description
; This data item is a pointer to _diffrn_detector.id in
the DIFFRN_DETECTOR category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_detector_axis.id'
_item.category_id diffrn_detector_axis
_item.mandatory_code no
_item_type.code code
save_
save__diffrn_detector_element.center[1]
_item_description.description
; The value of _diffrn_detector_element.center[1] is the X
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_fast
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[1]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_detector_element.center[2]
_item_description.description
; The value of _diffrn_detector_element.center[2] is the Y
component of the distortion-corrected beam centre in
millimetres from the (0, 0) (lower-left) corner of the
detector element viewed from the sample side.
The X and Y axes are the laboratory coordinate system
coordinates defined in the AXIS category measured
when all positioning axes for the detector are at their zero
settings. If the resulting X or Y axis is then orthogonal to the
detector, the Z axis is used instead of the orthogonal axis.
Because of ambiguity about the setting used to determine this
center, use of this data item is deprecated. The data item
_diffrn_data_frame.center_slow
which is referenced to the detector coordinate system and not
directly to the laboratory coordinate system should be used
instead.
;
_item.name '_diffrn_detector_element.center[2]'
_item.category_id diffrn_detector_element
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__diffrn_measurement_axis.id
_item_description.description
; This data item is a pointer to _diffrn_measurement.id in
the DIFFRN_MEASUREMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_measurement_axis.id'
_item.category_id diffrn_measurement_axis
_item.mandatory_code no
_item_type.code code
save_
######################### DEPRECATED CATEGORY #########################
#####################
# DIFFRN_FRAME_DATA #
#####################
save_diffrn_frame_data
_category.description
; Data items in the DIFFRN_FRAME_DATA category record
the details about each frame of data.
The items in this category are now in the
DIFFRN_DATA_FRAME category.
The items in the DIFFRN_FRAME_DATA category
are now deprecated. The items from this category
are provided as aliases in the 1.0 dictionary
or, in the case of _diffrn_frame_data.details,
in the 1.4 dictionary. THESE ITEMS SHOULD NOT
BE USED FOR NEW WORK.
The items from the old category are provided
in this dictionary for completeness
but should not be used or cited. To avoid
confusion, the example has been removed
and the redundant parent-child links to other
categories have been removed.
All _item.mandatory_code values have been changed to no
;
_category.id diffrn_frame_data
_category.mandatory_code no
loop_
_category_key.name '_diffrn_frame_data.id'
'_diffrn_frame_data.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
THE DIFFRN_FRAME_DATA category is deprecated and should not be used.
;
;
# EXAMPLE REMOVED #
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_frame_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.array_id'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code code
save_
save__diffrn_frame_data.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_STRUCTURE category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.binary_id'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code int
save_
save__diffrn_frame_data.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.detector_element_id'
_item.category_id diffrn_frame_data
_item.mandatory_code yes
_item_type.code code
save_
save__diffrn_frame_data.id
_item_description.description
; The value of _diffrn_frame_data.id must uniquely identify
each complete frame of data.
DEPRECATED -- DO NOT USE
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_diffrn_frame_data.id' diffrn_frame_data yes
_item_type.code code
save_
save__diffrn_frame_data.details
_item_description.description
; The value of _diffrn_data_frame.details should give a
description of special aspects of each frame of data.
DEPRECATED -- DO NOT USE
;
_item.name '_diffrn_frame_data.details'
_item.category_id diffrn_frame_data
_item.mandatory_code no
_item_type.code text
save_
################ END DEPRECATED SECTION ###########
####################
## ITEM_TYPE_LIST ##
####################
#
#
# The regular expressions defined here are not compliant
# with the POSIX 1003.2 standard as they include the
# '\n' and '\t' special characters. These regular expressions
# have been tested using version 0.12 of Richard Stallman's
# GNU regular expression library in POSIX mode.
# In order to allow presentation of a regular expression
# in a text field concatenate any line ending in a backslash
# with the following line, after discarding the backslash.
#
# A formal definition of the '\n' and '\t' special characters
# is most properly done in the DDL, but for completeness, please
# note that '\n' is the line termination character ('newline')
# and '\t' is the horizontal tab character. There is a formal
# ambiguity in the use of '\n' for line termination, in that
# the intention is that the equivalent machine/OS-dependent line
# termination character sequence should be accepted as a match, e.g.
#
# '\r' (control-M) under MacOS
# '\n' (control-J) under Unix
# '\r\n' (control-M control-J) under DOS and MS Windows
#
loop_
_item_type_list.code
_item_type_list.primitive_code
_item_type_list.construct
_item_type_list.detail
code char
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words ...
;
ucode uchar
'[_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]*'
; code item types/single words (case insensitive) ...
;
line char
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items ...
;
uline uchar
'[][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; char item types / multi-word items (case insensitive)...
;
text char
'[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*'
; text item types / multi-line text ...
;
binary char
;\n--CIF-BINARY-FORMAT-SECTION--\n\
[][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\
\n--CIF-BINARY-FORMAT-SECTION----
;
; binary items are presented as MIME-like ascii-encoded
sections in an imgCIF. In a CBF, raw octet streams
are used to convey the same information.
;
int numb
'-?[0-9]+'
; int item types are the subset of numbers that are the negative
or positive integers.
;
float numb
'-?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?'
; float item types are the subset of numbers that are the floating
point numbers.
;
any char
'.*'
; A catch all for items that may take any form...
;
yyyy-mm-dd char
;\
[0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9]?[0-9]\
((T[0-2][0-9](:[0-5][0-9](:[0-5][0-9](.[0-9]+)?)?)?)?\
([+-][0-5][0-9]:[0-5][0-9]))?
;
;
Standard format for CIF date and time strings (see
http://www.iucr.org/iucr-top/cif/spec/datetime.html),
consisting of a yyyy-mm-dd date optionally followed by
the character 'T' followed by a 24-hour clock time,
optionally followed by a signed time-zone offset.
The IUCr standard has been extended to allow for an optional
decimal fraction on the seconds of time.
Time is local time if no time-zone offset is given.
Note that this type extends the mmCIF yyyy-mm-dd type
but does not conform to the mmCIF yyyy-mm-dd:hh:mm
type that uses a ':' in place if the 'T' specified
by the IUCr standard. For reading, both forms should
be accepted, but for writing, only the IUCr form should
be used.
For maximal compatibility, the special time zone
indicator 'Z' (for 'zulu') should be accepted on
reading in place of '+00:00' for GMT.
;
#####################
## ITEM_UNITS_LIST ##
#####################
loop_
_item_units_list.code
_item_units_list.detail
#
'metres' 'metres'
'centimetres' 'centimetres (metres * 10^( -2)^)'
'millimetres' 'millimetres (metres * 10^( -3)^)'
'nanometres' 'nanometres (metres * 10^( -9)^)'
'angstroms' '\%Angstroms (metres * 10^(-10)^)'
'picometres' 'picometres (metres * 10^(-12)^)'
'femtometres' 'femtometres (metres * 10^(-15)^)'
#
'reciprocal_metres' 'reciprocal metres (metres^(-1)^)'
'reciprocal_centimetres'
'reciprocal centimetres ((metres * 10^( -2)^)^(-1)^)'
'reciprocal_millimetres'
'reciprocal millimetres ((metres * 10^( -3)^)^(-1)^)'
'reciprocal_nanometres'
'reciprocal nanometres ((metres * 10^( -9)^)^(-1)^)'
'reciprocal_angstroms'
'reciprocal \%Angstroms ((metres * 10^(-10)^)^(-1)^)'
'reciprocal_picometres'
'reciprocal picometres ((metres * 10^(-12)^)^(-1)^)'
#
'nanometres_squared' 'nanometres squared (metres * 10^( -9)^)^2^'
'angstroms_squared' '\%Angstroms squared (metres * 10^(-10)^)^2^'
'8pi2_angstroms_squared'
'8\p^2^ * \%Angstroms squared (metres * 10^(-10)^)^2^'
'picometres_squared' 'picometres squared (metres * 10^(-12)^)^2^'
#
'nanometres_cubed' 'nanometres cubed (metres * 10^( -9)^)^3^'
'angstroms_cubed' '\%Angstroms cubed (metres * 10^(-10)^)^3^'
'picometres_cubed' 'picometres cubed (metres * 10^(-12)^)^3^'
#
'kilopascals' 'kilopascals'
'gigapascals' 'gigapascals'
#
'hours' 'hours'
'minutes' 'minutes'
'seconds' 'seconds'
'microseconds' 'microseconds'
#
'degrees' 'degrees (of arc)'
'degrees_squared' 'degrees (of arc) squared'
#
'degrees_per_minute' 'degrees (of arc) per minute'
#
'celsius' 'degrees (of temperature) Celsius'
'kelvins' 'degrees (of temperature) Kelvin'
#
'counts' 'counts'
'counts_per_photon' 'counts per photon'
#
'electrons' 'electrons'
#
'electrons_squared' 'electrons squared'
#
'electrons_per_nanometres_cubed'
; electrons per nanometres cubed (electrons/(metres * 10^( -9)^)^(-3)^)
;
'electrons_per_angstroms_cubed'
; electrons per \%Angstroms cubed (electrons/(metres * 10^(-10)^)^(-3)^)
;
'electrons_per_picometres_cubed'
; electrons per picometres cubed (electrons/(metres * 10^(-12)^)^(-3)^)
;
'kilowatts' 'kilowatts'
'milliamperes' 'milliamperes'
'kilovolts' 'kilovolts'
#
'pixels_per_element' '(image) pixels per (array) element'
#
'arbitrary'
; arbitrary system of units.
;
#
loop_
_item_units_conversion.from_code
_item_units_conversion.to_code
_item_units_conversion.operator
_item_units_conversion.factor
###
'metres' 'centimetres' '*' 1.0E+02
'metres' 'millimetres' '*' 1.0E+03
'metres' 'nanometres' '*' 1.0E+09
'metres' 'angstroms' '*' 1.0E+10
'metres' 'picometres' '*' 1.0E+12
'metres' 'femtometres' '*' 1.0E+15
#
'centimetres' 'metres' '*' 1.0E-02
'centimetres' 'millimetres' '*' 1.0E+01
'centimetres' 'nanometres' '*' 1.0E+07
'centimetres' 'angstroms' '*' 1.0E+08
'centimetres' 'picometres' '*' 1.0E+10
'centimetres' 'femtometres' '*' 1.0E+13
#
'millimetres' 'metres' '*' 1.0E-03
'millimetres' 'centimetres' '*' 1.0E-01
'millimetres' 'nanometres' '*' 1.0E+06
'millimetres' 'angstroms' '*' 1.0E+07
'millimetres' 'picometres' '*' 1.0E+09
'millimetres' 'femtometres' '*' 1.0E+12
#
'nanometres' 'metres' '*' 1.0E-09
'nanometres' 'centimetres' '*' 1.0E-07
'nanometres' 'millimetres' '*' 1.0E-06
'nanometres' 'angstroms' '*' 1.0E+01
'nanometres' 'picometres' '*' 1.0E+03
'nanometres' 'femtometres' '*' 1.0E+06
#
'angstroms' 'metres' '*' 1.0E-10
'angstroms' 'centimetres' '*' 1.0E-08
'angstroms' 'millimetres' '*' 1.0E-07
'angstroms' 'nanometres' '*' 1.0E-01
'angstroms' 'picometres' '*' 1.0E+02
'angstroms' 'femtometres' '*' 1.0E+05
#
'picometres' 'metres' '*' 1.0E-12
'picometres' 'centimetres' '*' 1.0E-10
'picometres' 'millimetres' '*' 1.0E-09
'picometres' 'nanometres' '*' 1.0E-03
'picometres' 'angstroms' '*' 1.0E-02
'picometres' 'femtometres' '*' 1.0E+03
#
'femtometres' 'metres' '*' 1.0E-15
'femtometres' 'centimetres' '*' 1.0E-13
'femtometres' 'millimetres' '*' 1.0E-12
'femtometres' 'nanometres' '*' 1.0E-06
'femtometres' 'angstroms' '*' 1.0E-05
'femtometres' 'picometres' '*' 1.0E-03
###
'reciprocal_centimetres' 'reciprocal_metres' '*' 1.0E+02
'reciprocal_centimetres' 'reciprocal_millimetres' '*' 1.0E-01
'reciprocal_centimetres' 'reciprocal_nanometres' '*' 1.0E-07
'reciprocal_centimetres' 'reciprocal_angstroms' '*' 1.0E-08
'reciprocal_centimetres' 'reciprocal_picometres' '*' 1.0E-10
#
'reciprocal_millimetres' 'reciprocal_metres' '*' 1.0E+03
'reciprocal_millimetres' 'reciprocal_centimetres' '*' 1.0E+01
'reciprocal_millimetres' 'reciprocal_nanometres' '*' 1.0E-06
'reciprocal_millimetres' 'reciprocal_angstroms' '*' 1.0E-07
'reciprocal_millimetres' 'reciprocal_picometres' '*' 1.0E-09
#
'reciprocal_nanometres' 'reciprocal_metres' '*' 1.0E+09
'reciprocal_nanometres' 'reciprocal_centimetres' '*' 1.0E+07
'reciprocal_nanometres' 'reciprocal_millimetres' '*' 1.0E+06
'reciprocal_nanometres' 'reciprocal_angstroms' '*' 1.0E-01
'reciprocal_nanometres' 'reciprocal_picometres' '*' 1.0E-03
#
'reciprocal_angstroms' 'reciprocal_metres' '*' 1.0E+10
'reciprocal_angstroms' 'reciprocal_centimetres' '*' 1.0E+08
'reciprocal_angstroms' 'reciprocal_millimetres' '*' 1.0E+07
'reciprocal_angstroms' 'reciprocal_nanometres' '*' 1.0E+01
'reciprocal_angstroms' 'reciprocal_picometres' '*' 1.0E-02
#
'reciprocal_picometres' 'reciprocal_metres' '*' 1.0E+12
'reciprocal_picometres' 'reciprocal_centimetres' '*' 1.0E+10
'reciprocal_picometres' 'reciprocal_millimetres' '*' 1.0E+09
'reciprocal_picometres' 'reciprocal_nanometres' '*' 1.0E+03
'reciprocal_picometres' 'reciprocal_angstroms' '*' 1.0E+01
###
'nanometres_squared' 'angstroms_squared' '*' 1.0E+02
'nanometres_squared' 'picometres_squared' '*' 1.0E+06
#
'angstroms_squared' 'nanometres_squared' '*' 1.0E-02
'angstroms_squared' 'picometres_squared' '*' 1.0E+04
'angstroms_squared' '8pi2_angstroms_squared' '*' 78.9568
#
'picometres_squared' 'nanometres_squared' '*' 1.0E-06
'picometres_squared' 'angstroms_squared' '*' 1.0E-04
###
'nanometres_cubed' 'angstroms_cubed' '*' 1.0E+03
'nanometres_cubed' 'picometres_cubed' '*' 1.0E+09
#
'angstroms_cubed' 'nanometres_cubed' '*' 1.0E-03
'angstroms_cubed' 'picometres_cubed' '*' 1.0E+06
#
'picometres_cubed' 'nanometres_cubed' '*' 1.0E-09
'picometres_cubed' 'angstroms_cubed' '*' 1.0E-06
###
'kilopascals' 'gigapascals' '*' 1.0E-06
'gigapascals' 'kilopascals' '*' 1.0E+06
###
'hours' 'minutes' '*' 6.0E+01
'hours' 'seconds' '*' 3.6E+03
'hours' 'microseconds' '*' 3.6E+09
#
'minutes' 'hours' '/' 6.0E+01
'minutes' 'seconds' '*' 6.0E+01
'minutes' 'microseconds' '*' 6.0E+07
#
'seconds' 'hours' '/' 3.6E+03
'seconds' 'minutes' '/' 6.0E+01
'seconds' 'microseconds' '*' 1.0E+06
#
'microseconds' 'hours' '/' 3.6E+09
'microseconds' 'minutes' '/' 6.0E+07
'microseconds' 'seconds' '/' 1.0E+06
###
'celsius' 'kelvins' '-' 273.0
'kelvins' 'celsius' '+' 273.0
###
'electrons_per_nanometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E+03
'electrons_per_nanometres_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+09
#
'electrons_per_angstroms_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-03
'electrons_per_angstroms_cubed'
'electrons_per_picometres_cubed' '*' 1.0E+06
#
'electrons_per_picometres_cubed'
'electrons_per_nanometres_cubed' '*' 1.0E-09
'electrons_per_picometres_cubed'
'electrons_per_angstroms_cubed' '*' 1.0E-06
###
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.7.10 2014-04-25
; Additions of esd's to polarization tags. Change to NeXus mapping to use
NXtransformations instead of NXpoise (HJB)
+ Add _diffrn_radiation.polarisn_norm_esd,
_diffrn_radiation.polarisn_ratio_esd,
_diffrn_radiation.polarizn_source_norm_esd,
_diffrn_radiation.polarizn_source_ratio_esd,
_diffrn_radiation.polarizn_Stokes_I_esd,
_diffrn_radiation.polarizn_Stokes_Q_esd,
_diffrn_radiation.polarizn_Stokes_U_esd,
_diffrn_radiation.polarizn_Stokes_V_esd,
_diffrn_scan_frame.polarizn_Stokes_I_esd,
_diffrn_scan_frame.polarizn_Stokes_Q_esd,
_diffrn_scan_frame.polarizn_Stokes_U_esd,
_diffrn_scan_frame.polarizn_Stokes_V_esd.
+ Change NeXus mapping for ARRAY_STRUCTURE_LIST
ARRAY_STRUCTURE_LIST_AXIS, AXIS,
DIFFRN_DETECTOR_AXIS, DIFFRN_MEASUREMENT_AXIS,
DIFFRN_SCAN_FRAME_AXIS.
;
1.7.9 2014-04-05
; Corrections to Stokes parameter description. (HJB)
+ Clarify the meaning of _diffrn_radiation.polarizn_Stokes_I
and _diffrn_scan_frame.polarizn_Stokes_I to explicitly include non-polarized
component.
+ Provide missing factor of 2 in _diffrn_radiation.polarizn_Stokes_V
description and _diffrn_scan_frame.polarizn_Stokes_V description.
;
1.7.8 2014-02-22
; Minor changes to NeXus mapping. (HJB)
+ Conform NeXus mapping of DIFFRN_DETECTOR to neXus
NXdetector base class terminology
+ Add _diffrn_detector.gain_setting to handle
the reverse mapping fron NeXus of the equivalent field in NXdetector.
;
1.7.7 2014-02-22
; Major changes to NeXus mapping to conform to JS functional
mapping prototype, add Stoke parameter tags for polarization
and beam intensity, and add an new tag for FEL axes (HJB)
+ Add
_axis.equipment_component,
_diffrn_radiation.polarizn_Stokes_I,
_diffrn_radiation.polarizn_Stokes_Q,
_diffrn_radiation.polarizn_Stokes_U,
_diffrn_radiation.polarizn_Stokes_V,
_diffrn_scan_frame.polarizn_Stokes_I,
_diffrn_scan_frame.polarizn_Stokes_Q,
_diffrn_scan_frame.polarizn_Stokes_U,
_diffrn_scan_frame.polarizn_Stokes_V.
+ Remove erroneous type code from _diffrn_scan_frame_monitor.value.
+ Update dictionary version
;
1.7.6 2013-10-29
; To avoid a conflict with PDB software, remove the null value
enumeration for _variant.role (HJB)
;
1.7.5 2013-10-27
; At request of JW for the PDB move _category.NX_mapping_details
to be adjacent to other category tags. (HJB)
;
1.7.4 2013-10-23
; Minor cleanup and rmeove spurious tag
+ remove spurious _array_structure_list_section.array_set_id
references. (JS)
+ Change case of category names to conform to PDB conventions. (JW)
;
1.7.3 2013-10-15
; Major cleanup of dictionary typos, misplaced loops, etc
by John Westbrook
+ Change _item.mandatory_code of all *.variant to implicit
+ Add _diffrn_refln.id and _diffrn_refln.diffrn_id
+ Correct many _item.name values that were wrong or missing
quote marks
;
1.7.2 2013-10-07
; Add FEL detector positioning tags and change back to NXgoniometer
+ Add
_axis.rotation_axis and
_axis.rotation and
+ Change NXsample back to NXgoniometer
;
1.7.1 2013-08-10
; Minor cleanup (HJB)
+ Correction to description of
_diffrn_data_frame.array_section_id
+ Change NXgoniometer to NXsample
+ Fix typos in NeXus mappings
;
1.7 2013-06-18
; Additions to start merge of CBF, HDF5 and NeXus (HJB)
+ Define new ARRAY_STRUCTURE_LIST_SECTION category
+ Add new _category.NX_mapping_details DDL tag to carry
details on NeXus category mappings.
+ Define new tags _array_structure_list_section.array_id,
_array_structure_list_section.id,
_array_structure_list_section.index,
_array_structure_list_section.end,
_array_structure_list_section.start,
_array_structure_list_section.stride,
_array_structure_list_section.variant,
_diffrn_data_frame.array_section_id,
_diffrn_detector.layer_thickness,
_map_segment.array_section_id,
_map_segment.mask_array_section_id
;
1.6.4 2011-07-02
; Corrections to support DLS Dectris header as per G. Winter (HJB)
+ Define new tags _diffrn_scan.time_period,
_diffrn_scan.time_rstrt_incr,
_diffrn_scan_frame.time_period,
_diffrn_scan_frame.time_rstrt_incr
+ fix bad category name in loop in _diffrn_detector.id
+ remove stray text field terminator at line 4642
+ fix unquoted tag as a value in _diffrn_scan_frame_monitor.id
+ make formerly mandatory and implicit deprecated items non-mandatory
;
1.6.3 2010-08-26
; Cummulative corrections from 1.6.0, 1, 2 drafts (HJB)
+ Move descriptive dictionary comments into
_datablock.description with catgeory tree described
+ add default _array_data.array_id value of 1
+ add option of CBF_BACKGROUND_OFFSET_DELTA compression
+ add VARIANT category and tags
+ add DIFFRN_SCAN_FRAME_MONITOR category
;
1.5.4 2007-07-28
; Typographics corrections (HJB)
+ Corrected embedded degree characters to \%
+ Corrected embedded Aring to \%A
+ Added trailing ^ for a power
+ Removed 2 cases of a space after an underscore
in tag name.
;
1.5.3 2007-07-08
; Changes to support SLS miniCBF and suggestions
from the 24 May 07 BNL imgCIF workshop (HJB)
+ Added new data items
'_array_data.header_contents',
'_array_data.header_convention',
'_diffrn_data_frame.center_fast',
'_diffrn_data_frame.center_slow',
'_diffrn_data_frame.center_units',
'_diffrn_measurement.sample_detector_distance',
'_diffrn_measurement.sample_detector_voffset
+ Deprecated data items
'_diffrn_detector_element.center[1]',
'_diffrn_detector_element.center[2]'
+ Added comments and example on miniCBF
+ Changed all array_id data items to implicit
;
1.5.2 2007-05-06
; Further clarifications of the coordinate system. (HJB)
;
1.5.1 2007-04-26
; Improve defintion of X-axis to cover the case of no goniometer
and clean up more line folds (HJB)
;
1.5 2007-07-25
; This is a cummulative list of the changes proposed since the
imgCIF workshop in Hawaii in July 2006. It is the result
of contributions by H. J. Bernstein, A. Hammersley,
J. Wright and W. Kabsch.
2007-02-19 Consolidated changes (edited by HJB)
+ Added new data items
'_array_structure.compression_type_flag',
'_array_structure_list_axis.fract_displacement',
'_array_structure_list_axis.displacement_increment',
'_array_structure_list_axis.reference_angle',
'_array_structure_list_axis.reference_displacement',
'_axis.system',
'_diffrn_detector_element.reference_center_fast',
'_diffrn_detector_element.reference_center_slow',
'_diffrn_scan_axis.reference_angle',
'_diffrn_scan_axis.reference_displacement',
'_map.details', '_map.diffrn_id',
'_map.entry_id', '_map.id',
'_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.
+ Change type of
'_array_structure.byte_order' and
'_array_structure.compression_type'
to ucode to make these values case-insensitive
+ Add values 'packed_v2' and 'byte_offset' to enumeration of values for
'_array_structure.compression_type'
+ Add to definitions for the binary data type to handle new compression
types, maps, and a variety of new axis types.
2007-07-25 Cleanup of typos for formal release (HJB)
+ Corrected text fields for reference_ tag descriptions that
were off by one column
+ Fix typos in comments listing fract_ tags
+ Changed name of release from 1.5_DRAFT to 1.5
+ Fix unclosed text fields in various map definitions
;
1.4 2006-07-04
; This is a change to reintegrate all changes made in the course of
publication of ITVG, by the RCSB from April 2005 through
August 2008 and changes for the 2006 imgCIF workshop in
Hawaii.
2006-07-04 Consolidated changes for the 2006 imgCIF workshop (edited by HJB)
+ Correct type of '_array_structure_list.direction' from 'int' to 'code'.
+ Added new data items suggested by CN
'_diffrn_data_frame.details'
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size and
'_array_intensities.pixel_binning_method
+ Added deprecated item for completeness
'_diffrn_frame_data.details'
+ Added entry for missing item in contents list
'_array_structure_list_axis.displacement'
+ Added new MIME type X-BASE32K based on work by VL, KM, GD, HJB
+ Correct description of MIME boundary delimiter to start in
column 1.
+ General cleanup of text fields to conform to changes for ITVG
by removing empty lines at start and finish of text field.
+ Amend example for ARRAY_INTENSITIES to include binning.
+ Add local copy of type specification (as 'code') for all children
of '_diffrn.id'.
+ For consistency, change all references to 'pi' to '\p' and all
references to 'Angstroms' to '\%Angstroms'.
+ Clean up all powers to use IUCr convention of '^power^', as in
'10^3^' for '10**3'.
+ Update 'yyyy-mm-dd' type regex to allow truncation from the right
and improve comments to explain handling of related mmCIF
'yyyy-mm-dd:hh:mm' type, and use of 'Z' for GMT time zone.
2005-03-08 and
2004-08-08 fixed cases where _item_units.code used
instead of _item_type.code (JDW)
2004-04-15 fixed item ordering in
_diffrn_measurement_axis.measurement_id
added sub_category 'vector' (JDW)
;
1.3.2 2005-06-25
; 2005-06-25 ITEM_TYPE_LIST: code, ucode, line, uline regexps updated
to those of current mmCIF; float modified by allowing integers
terminated by a point as valid. The 'time' part of
yyyy-mm-dd types made optional in the regexp. (BM)
2005-06-17 Minor corrections as for proofs for IT G Chapter 4.6
(NJA)
2005-02-21 Minor corrections to spelling and punctuation
(NJA)
2005-01-08 Changes as per Nicola Ashcroft.
+ Updated example 1 for DIFFRN_MEASUREMENT to agree with mmCIF.
+ Spelled out "micrometres" for "um" and "millimetres" for "mm".
+ Removed phrase "which may be stored" from ARRAY_STRUCTURE
description.
+ Removed unused 'byte-offsets' compressions and updated
cites to ITVG for '_array_structure.compression_type'.
(HJB)
;
1.3.1 2003-08-13
;
Changes as per Frances C. Bernstein.
+ Identify initials.
+ Adopt British spelling for centre in text.
+ Set \p and \%Angstrom and powers.
+ Clean up commas and unclear wordings.
+ Clean up tenses in history.
Changes as per Gotzon Madariaga.
+ Fix the ARRAY_DATA example to align '_array_data.binary_id'
and X-Binary-ID.
+ Add a range to '_array_intensities.gain_esd'.
+ In the example of DIFFRN_DETECTOR_ELEMENT,
'_diffrn_detector_element.id' and
'_diffrn_detector_element.detector_id' interchanged.
+ Fix typos for direction, detector and axes.
+ Clarify description of polarisation.
+ Clarify axes in '_diffrn_detector_element.center[1]'
'_diffrn_detector_element.center[2]'.
+ Add local item types for items that are pointers.
(HJB)
;
1.3.0 2003-07-24
;
Changes as per Brian McMahon.
+ Consistently quote tags embedded in text.
+ Clean up introductory comments.
+ Adjust line lengths to fit in 80 character window.
+ Fix several descriptions in AXIS category which
referred to '_axis.type' instead of the current item.
+ Fix erroneous use of deprecated item
'_diffrn_detector_axis.id' in examples for
DIFFRN_SCAN_AXIS.
+ Add deprecated items '_diffrn_detector_axis.id'
and '_diffrn_measurement_axis.id'.
(HJB)
;
1.2.4 2003-07-14
;
Changes as per I. David Brown.
+ Enhance descriptions in DIFFRN_SCAN_AXIS to make them less
dependent on the descriptions in DIFFRN_SCAN_FRAME_AXIS.
+ Provide a copy of the deprecated DIFFRN_FRAME_DATA
category for completeness.
(HJB)
;
1.2.3 2003-07-03
;
Cleanup to conform to ITVG.
+ Correct sign error in ..._cubed units.
+ Correct '_diffrn_radiation.polarisn_norm' range.
(HJB)
;
1.2.2 2003-03-10
;
Correction of typos in various DIFFRN_SCAN_AXIS descriptions.
(HJB)
;
1.2.1 2003-02-22
;
Correction of ATOM_ for ARRAY_ typos in various descriptions.
(HJB)
;
1.2 2003-02-07
;
Corrections to encodings (remove extraneous hyphens) remove
extraneous underscore in '_array_structure.encoding_type'
enumeration. Correct typos in items units list. (HJB)
;
1.1.3 2001-04-19
;
Another typo corrections by Wilfred Li, and cleanup by HJB.
;
1.1.2 2001-03-06
;
Several typo corrections by Wilfred Li.
;
1.1.1 2001-02-16
;
Several typo corrections by JW.
;
1.1 2001-02-06
;
Draft resulting from discussions on header for use at NSLS. (HJB)
+ Change DIFFRN_FRAME_DATA to DIFFRN_DATA_FRAME.
+ Change '_diffrn_detector_axis.id' to '_diffrn_detector_axis.detector_id'.
+ Add '_diffrn_measurement_axis.measurement_device' and change
'_diffrn_measurement_axis.id' to
'_diffrn_measurement_axis.measurement_id'.
+ Add '_diffrn_radiation.div_x_source', '_diffrn_radiation.div_y_source',
'_diffrn_radiation.div_x_y_source',
'_diffrn_radiation.polarizn_source_norm',
'_diffrn_radiation.polarizn_source_ratio', '_diffrn_scan.date_end',
'_diffrn_scan.date_start', '_diffrn_scan_axis.angle_rstrt_incr',
'_diffrn_scan_axis.displacement_rstrt_incr',
'_diffrn_scan_frame_axis.angle_increment',
'_diffrn_scan_frame_axis.angle_rstrt_incr',
'_diffrn_scan_frame_axis.displacement',
'_diffrn_scan_frame_axis.displacement_increment',and
'_diffrn_scan_frame_axis.displacement_rstrt_incr'.
+ Add '_diffrn_measurement.device' to category key.
+ Update yyyy-mm-dd to allow optional time with fractional seconds
for time stamps.
+ Fix typos caught by RS.
+ Add ARRAY_STRUCTURE_LIST_AXIS category, and use concept of axis sets to
allow for coupled axes, as in spiral scans.
+ Add examples for fairly complete headers thanks to R. Sweet and P.
Ellis.
;
1.0 2000-12-21
;
Release version - few typos and tidying up. (BM & HJB)
+ Move ITEM_TYPE_LIST, ITEM_UNITS_LIST and DICTIONARY_HISTORY to end
of dictionary.
+ Alphabetize dictionary.
;
0.7.1 2000-09-29
;
Cleanup fixes. (JW)
+ Correct spelling of DIFFRN_MEASUREMENT_AXIS in '_axis.id'
+ Correct ordering of uses of '_item.mandatory_code' and
'_item_default.value'.
;
0.7.0 2000-09-09
;
Respond to comments by I. David Brown. (HJB)
+ Add further comments on '\n' and '\t'.
+ Update ITEM_UNITS_LIST by taking section from mmCIF dictionary
and adding metres. Change 'meter' to 'metre' throughout.
+ Add missing enumerations to '_array_structure.compression_type'
and make 'none' the default.
+ Remove parent-child relationship between
'_array_structure_list.index' and '_array_structure_list.precedence'.
+ Improve alphabetization.
+ Fix '_array_intensities.gain_esd' related function.
+ Improve comments in AXIS.
+ Fix DIFFRN_FRAME_DATA example.
+ Remove erroneous DIFFRN_MEASUREMENT example.
+ Add '_diffrn_measurement_axis.id' to the category key.
;
0.6.0 1999-01-14
;
Remove redundant information for ENC_NONE data. (HJB)
+ After the D5 remove binary section identifier, size and
compression type.
+ Add Control-L to header.
;
0.5.1 1999-01-03
;
Cleanup of typos and syntax errors. (HJB)
+ Cleanup example details for DIFFRN_SCAN category.
+ Add missing quote marks for '_diffrn_scan.id' definition.
;
0.5 1999-01-01
;
Modifications for axis definitions and reduction of binary header. (HJB)
+ Restore '_diffrn_detector.diffrn_id' to DIFFRN_DETECTOR KEY.
+ Add AXIS category.
+ Bring in complete DIFFRN_DETECTOR and DIFFRN_MEASUREMENT categories
from cif_mm.dic for clarity.
+ Change '_array_structure.encoding_type' from type code to uline and
added X-Binary-Element-Type to MIME header.
+ Add detector beam centre '_diffrn_detector_element.center[1]' and
'_diffrn_detector_element.center[2]'.
+ Correct item name of '_diffrn_refln.frame_id'.
+ Replace reference to '_array_intensities.undefined' by
'_array_intensities.undefined_value'.
+ Replace references to '_array_intensity.scaling' with
'_array_intensities.scaling'.
+ Add DIFFRN_SCAN... categories.
;
0.4 1998-08-11
;
Modifications to the 0.3 imgCIF draft. (HJB)
+ Reflow comment lines over 80 characters and corrected typos.
+ Update examples and descriptions of MIME encoded data.
+ Change name to cbfext98.dic.
;
0.3 1998-07-04
;
Modifications for imgCIF. (HJB)
+ Add binary type, which is a text field containing a variant on
MIME encoded data.
+ Change type of '_array_data.data' to binary and specify internal
structure of raw binary data.
+ Add '_array_data.binary_id', and make
'_diffrn_frame_data.binary_id' and '_array_intensities.binary_id'
into pointers to this item.
;
0.2 1997-12-02
;
Modifications to the CBF draft. (JW)
+ Add category hierarchy for describing frame data developed from
discussions at the BNL imgCIF Workshop Oct 1997. The following
changes are made in implementing the workshop draft. Category
DIFFRN_array_data is renamed to DIFFRN_FRAME_DATA. Category
DIFFRN_FRAME_TYPE is renamed to DIFFRN_DETECTOR_ELEMENT. The
parent item for '_diffrn_frame_data.array_id' is changed from
'_array_structure_list.array_id' to '_array_structure.id'. Item
'_diffrn_detector.array_id' is deleted.
+ Add data item '_diffrn_frame_data.binary_id' to identify data
groups within a binary section. The formal identification of the
binary section is still fuzzy.
;
0.1 1997-01-24
;
First draft of this dictionary in DDL 2.1 compliant format by John
Westbrook (JW). This version is adapted from the Crystallographic
Binary File (CBF) Format Draft Proposal provided by Andy Hammersley
(AH).
Modifications to the CBF draft. (JW)
+ In this version the array description has been cast in the categories
ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. These categories
have been generalized to describe array data of arbitrary dimension.
+ Array data in this description are contained in the category
ARRAY_DATA. This departs from the CBF notion of data existing
in some special comment. In this description, data are handled as an
ordinary data item encapsulated in a character data type. Although
data this manner deviates from CIF conventions, it does not violate
any DDL 2.1 rules. DDL 2.1 regular expressions can be used to define
the binary representation which will permit some level of data
validation. In this version, the placeholder type code "any" has
been used. This translates to a regular expression which will match
any pattern.
It should be noted that DDL 2.1 already supports array data objects
although these have not been used in the current mmCIF dictionary.
It may be possible to use the DDL 2.1 ITEM_STRUCTURE and
ITEM_STRUCTURE_LIST categories to provide the information that is
carried in by the ARRAY_STRUCTURE and ARRAY_STRUCTURE_LIST. By
moving the array structure to the DDL level it would be possible to
define an array type as well as a regular expression defining the
data format.
+ Multiple array sections can be properly handled within a single
datablock.
;
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