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########################
## DICTIONARY_HISTORY ##
########################
##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.7.11 #
# of 2014-07-05 #
# ################################################################### #
# # *** 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.array_section_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 1.7.11
_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.
;
########################
## DICTIONARY_HISTORY ##
########################
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
1.7.11 2014-07-05
; Changes for CBFlib 0.9.6 release (HJB)
+ Remove _array_structure_list.array_section_id
+ Revisions to _category.NX_mapping_details in most categories for
array sections.
+ Change to uniform use of entry:NXentry
+ Change to uniform use of identification of NXdetector by detector
element
+ Change to uniform use of data_ARRAYID_BINARYID
+ Add _array_structure_list.array_section_id
+ Add _map_segment.mask_array_section_id
;
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'.