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cif_img.dic
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#\#CIF_2.0
data_CIF_IMG.DIC
_dictionary.title Cif_img.dic
_dictionary.class Instance
_dictionary.version 1.8.6
_dictionary.date 2022-05-11
_dictionary.ddl_conformance 3.14.0
_dictionary.namespace CifCore
_description.text
;##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.8.6 #
# of 2022-05-11 #
# #
# #
# ################################################################### #
# # *** WARNING *** THIS IS A DRAFT FOR DISCUSSION *** WARNING *** # #
# # SUBJECT TO CHANGE WITHOUT NOTICE # #
# # SEND COMMENTS TO imgcif-l@iucr.org CITING THE VERSION # #
# ################################################################### #
# This draft edited by B. McMahon and H. J. Bernstein #
# #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from a 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 is being prepared in support of the 2021 #
# revisions to ITVG, and was drafted by Herbert J. Bernstein and #
# incorporates comments by James Hester, 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 and reflects comments in #
# Bernstein, H. J., Foerster, A., Bhowmick, A., Brewster, A. S., #
# Brockhauser, S., Gelisio, L., Hall, D. R., Leonarski, F., Mariani, V., #
# Santoni, G., Vonrhein, C. & Winter, G. (2020). "Gold Standard for #
# Macromolecular Crystallography Diffraction Data", IUCrJ, 7, 784--792, #
# https://doi.org/10.1107/S2052252520008672, #
# https://doi.org//10.1107/S2052252520008672/ti5018sup1.pdf, #
# https://doi.org//10.1107/S2052252520008672/ti5018sup2.pdf #
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
# SUB_CATEGORY
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
# _array_data.external_data_id
# _array_data.header_contents
# _array_data.header_convention
# _array_data.variant
#
# category ARRAY_DATA_EXTERNAL_DATA
#
# _array_data_external_data.archive_format
# _array_data_external_data.archive_path
# _array_data_external_data.format
# _array_data_external_data.frame
# _array_data_external_data.id
# _array_data_external_data.path
# _array_data_external_data.uri
# _array_data_external_data.variant
# _array_data_external_data.version
#
# 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.overload
# _array_intensities.pixel_fast_bin_size
# _array_intensities.pixel_slow_bin_size
# _array_intensities.pixel_binning_method
# _array_intensities.scaling
# _array_intensities.undefined_value
# _array_intensities.underload
# _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.end
# _array_structure_list_section.id
# _array_structure_list_section.index
# _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.angular_pitch
# _array_structure_list_axis.displacement
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.fract_displacement
# _array_structure_list_axis.fract_displacement_increment
# _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.beam_width
# _diffrn_radiation.beam_height
# _diffrn_radiation.beam_flux
# _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.polarisn_norm_esd
# _diffrn_radiation.polarisn_ratio_esd
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_norm_esd
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.polarizn_source_ratio_esd
# _diffrn_radiation.polarizn_Stokes_I
# _diffrn_radiation.polarizn_Stokes_Q
# _diffrn_radiation.polarizn_Stokes_U
# _diffrn_radiation.polarizn_Stokes_V
# _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.variant
# _diffrn_radiation.wavelength_id
# _diffrn_radiation.xray_symbol
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
# _diffrn_refln.variant
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_end_estimated
# _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_COLLECTION
#
# _diffrn_scan_collection.details
# _diffrn_scan_collection.scan_id
# _diffrn_scan_collection.type
# _diffrn_scan_collection.translation_width
# _diffrn_scan_collection.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.frame_id
# _diffrn_scan_frame_monitor.integration_time
# _diffrn_scan_frame_monitor.monitor_value
# _diffrn_scan_frame_monitor.scan_id
# _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
# _diffrn_scan_frame_monitor.value
#
# ***DEPRECATED*** category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
# _diffrn_frame_data.details
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#Category Group Table:
+--------------------------------------------------------------------------------------------------------------------+
|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 need 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_DATA_EXTERNAL_DATA | Data items in the ARRAY_DATA_EXTERNAL_DATA category | ||
| || | | | record information needed to refer to data arrays in | ||
| || | | | external datasets. All necessary metadata must also | ||
| || | | | be copied or linked. | ||
| || | |-----------------------------------------------------------------------------------------| ||
| || +---------------------------------------------------------------------------------------------+ ||
| |+-------------------------------------------------------------------------------------------------+|
| ||--------------------------+----------------------------------------------------------------------||
| || 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 NeXus/HDF5 McStas 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_COLLECTION | Data items in the DIFFRN_SCAN_COLLECTION category describe the | ||
| || | | | type of collection strategy involved in each scan. | ||
| || +---------------------------------------------------------------------------------------------+ ||
| ||-------------------------------------------------------------------------------------------------||
| || +---------------------------------------------------------------------------------------------+ ||
| || | | 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 map. 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. ||
| |+-------------------------------------------------------------------------------------------------+|
+--------------------------------------------------------------------------------------------------------------------+
;
save_HEAD
_definition.id HEAD
_definition.scope Category
_definition.class Head
_description.text
;
The HEAD category is the parent category of all definitions in the
dictionary
;
_name.category_id HEAD
_name.object_id HEAD
_import.get
[
{
'dupl':Ignore
'file':https://www.iucr.org/__data/iucr/cif/dictionaries/cif_core_3.2.0.dic
'mode':Full 'save':cif_core
}
]
save_
save_ARRAY_DATA
_definition.id ARRAY_DATA
_definition.scope Category
_definition.class Loop
_description.text
;
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 need 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, beamline-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.
;
_name.category_id HEAD
_name.object_id ARRAY_DATA
_name.ddl2_mandatory no
loop_
_category_key.name
'_array_data.array_id'
'_array_data.binary_id'
'_array_data.variant'
loop_
_description_example.case
_description_example.detail
;
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 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.
;
;
###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----
;
;
;
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.
;
save_
save_array_data.array_id
_definition.id '_array_data.array_id'
_description.text
;
This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
If not given, it defaults to 1.
;
_name.category_id array_data
_name.object_id array_id
_name.linked_item_id '_array_structure.id'
_name.ddl2_mandatory implicit
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Text
_type.ddl2_code code
_enumeration.default 1
save_
save_array_data.binary_id
_definition.id '_array_data.binary_id'
_description.text
;
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.
;
_name.category_id array_data
_name.object_id binary_id
_name.ddl2_mandatory implicit
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Integer
_type.ddl2_code int
_enumeration.range 1:
_enumeration.default 1
save_
save_array_data.data
_definition.id '_array_data.data'
_description.text
;
The value of _array_data.data contains the array data
encapsulated in a STAR string. The value of this item is
required unless a value is given for
_array_data.external_data_id instead, in which
case, a null value of '.' should be given here.
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--, where \n represents the system
newline character(s)).
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
(e.g. conversions="X-CBF_PACKED flat").
In such cases the _array_structure.compression_type_flag
should also be present with the corresponding value.
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
image will be treated as one long row.
Note that X-CBF_CANONICAL and X-CBF_PACKED are
slower but more efficient compressions than 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