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Cifsas dictionary
- Subject: Cifsas dictionary
- From: Marco <Malfois@embl-hamburg.de>
- Date: Mon, 24 Aug 1998 09:55:19 +0200
- Organization: EMBL
Dear All, below you will find a draft of a one-dimensional SAS data format prepared following the discussions at the Denver X-ray conference (Aug'97), Workshop at NIST (Jan'98), canSAS'98 (Grenoble, Feb'98) and ACA'98 (Arlington, July'98) meetings. The idea was to have a simple interchangeable format which can be written/read by the data aquisition and analysis software. A consensus seemed to be reached on an ASCII format for one-dimensional data which includes: - a self-described header containing all relevant information about the sample and instrumental conditions; - raw or reduced data in a table form. The above structure was implemented by defining a dictionary serving as a common basis to make the files self describing. This dictionary was realized as an extension of CIF (Crystallographic Information File), which is a standard means of information interchange in crystallography. Similar "extension" approach has been developed, e.g. for the powder crystallography data. Adhering to CIF allows to use numerous public domain programs developed for this format (you may read all about it at the UICr WWW page). Please note that the draft below concerns only 1D data. For 2D files, a portable binary format would probably be required, which is out of scope of the current project. Your comments/suggestions/extensions/criticism are welcome. Please put them on the SAS listserver or send directly to Malfois@EMBL-Hamburg.DE or Svergun@EMBL-Hamburg.DE. If a consensus will be reached, the project will be extended to develop relevant tools for this format. Any standard is meaningful only if it is going to be used! The information below includes: 1. A short description of the names used 2. An example of a sasCIF file 3. A "sasCIF extension" to a CIF dictionary.
sasCIF dictionary (draft)
Description of the names used
M.Malfois, D.Svergun, July 1998
PUBLIC INFORMATION
### All included in the core CIF dictionary
BLOCK INFORMATION
# Some relevant CIF dictionary entries are also listed
_audit_Block_code_ Identifies uniquely the current data block
_audit_Creation_date_
_audit_Update_Record_ History
_sas_block_data_id Uniquely identifies the current SAS data block
SOURCE INFORMATION
_diffrn_radiation_source X-ray tube, neutron reactor...
_diffrn_radiation_probe Source of radiation (X-rays/Neutrons)
_diffrn_radiation_wavelength radiation wavelength in A.
_diffrn_radiation_monochromator Its type
# Assumed: x=equatorial direction, y=azimuthal direction
_sas_beam_collimation_slit_x Collimation slits in cm
_sas_beam_collimation_slit_y
_sas_beam_size_x Beam size on the sample in cm
_sas_beam_size_y
_sas_beam_divergence_x Beam divergency in radians
_sas_beam_divergence_y
_sas_beam_collimation_distance In cm
_sas_beam_sample_detector In cm
_sas_beam_delta_lambda (Delta lambda) /lambda
DETECTOR INFORMATION
_diffrn_detector general class of detector
_diffrn_detector_type Model or name of the detector used
_sas_det_beamstop_x Beamstop size on X, cm
_sas_det_beamstop_y Beamstop size on Y, cm
_sas_det_pixnum_x Number of detector pixels in X direction
_sas_det_pixnum_y Number of detector pixels in Y direction
_sas_det_pixsiz_x Pixel size, X direction, cm
_sas_det_pixsiz_y Pixel size, Y direction, cm
_sas_det_center_x Beam center, X coordinate in cm from left
_sas_det_center_y Beam center, Y coordinate in cm from bottom
_sas_det_rad_step Radial step to group pixels for
circular average (cm)
_sas_det_mer_fact # of channels merged together (1D-detector)
_sas_det_rotation Tilt of the detector (degrees)
_sas_det_sector_width In degrees (for sectorial average)
_sas_det_sector_orientation In degrees with respect to X direction
SAMPLE INFORMATION
_chemical_compound_source_
_diffrn_ambient_temperature temperature in K
_diffrn_ambient_environment air, vacuum...
_sas_sample_name Sample description
_sas_sample_concentration In g/l
_sas_sample_thickness In cm
_sas_sample_transmission
_sas_sample_time For kinematic measurements
_sas_sample_strain
_sas_sample_pressure any other parameters ???
_sas_sample_orientation Sample normal/beam
_sas_sample_monitor sample calibration channel value
_sas_sample_buffer_composition
_sas_sample_buffer_pH
_sas_sample_matrix_monitor matrix calibration channel value
_sas_sample_exposure measurement exposure time
TREATMENT INFORMATION
_sas_trt_detres_made data normalized against response Y/N
_sas_trt_detres_block Detector response data block
_sas_trt_matrix_made Matrix/buffer scattering subtracted Y/N
_sas_trt_matrix_block Matrix/buffer scattering block
_sas_trt_matrix_transmission Transmission of the matrix/buffer
_sas_trt_background_made Background subtracted Y/N
_sas_trt_background_block Background scattering block
_sas_trt_background_transmission Transmission of empty cell
_sas_trt_raw_data_file acquisition data file(s)
_sas_trt_raw_data_date date/time of raw data file
_sas_trt_date date/time of primary data treatment
DATA INFORMATION
_sas_data_type Possible types: $Sample, $Matrix,
$Detector, $Background
_sas_data_title
_sas_data_momentum_transfer momentum transfer (Q,q,s,S,h,k,m....)
_sas_data_momentum_factor Scaling factor of the above quantity to
4*pi sin(th)/lam [A-1]
_sas_data_intensity scattering intensity
_sas_data_stat_error standard deviation
_sas_data_syst_error e.g. from radial average etc
_sas_data_scaling_factor Scaling factor for the intensity and errors
_sas_data_group_factor # of pixels contributing to this point
_sas_data_resolution Width of Gaussian resolution function
#####################################################
# Example file illustrating description #
# of a small-angle scattering experiment #
# with data names from the core CIF #
# and sasCIF extension dictionaries #
# #
# Warning: was NOT checked against the CIF rules, #
# just gives impression on how a sasCIF #
# file would look like ... #
#####################################################
data_TEST_publ
_audit_block_code 1998-07-09_Exa_for_sasCIF
_audit_creation_date 1998-07-08
_audit_creation_method "from PD example file"
loop_ _publ_contact_author_name
_publ_contact_author_email
_publ_contact_author_phone
_publ_contact_author_fax
" M.Malfois" ,
Malfois@EMBL-Hamburg.De ,
+49(40)89902148 ,
+49(40)89902149 ,
" D.Svergun" ,
Svergun@EMBL-Hamburg.De ,
+49(40)89902125 ,
+49(40)89902149 ,
_publ_contact_author_adress
; EMBL c/o DESY
Notkestrasse 85
D-22603 Hamburg
Germany
;
_publ_section_title "Chicken egg white lysozyme"
_diffrn_radiation_source "Storage ring DORIS, beamline X33"
_diffrn_radiation_probe "Synchrotron radiation X-rays"
_diffrn_radiation_wavelength 1.5
_diffrn_radiation_monochromator "Bent crystal"
_sas_beam_size_x 0.2
_sas_beam_size_y 0.5
_sas_beam_sample_detector 150
_diffrn_detector "Gas-filled proportional"
_diffrn_detector_type Quadrant
_sas_det_beamstop_x 0.5
_sas_det_beamstop_y 0.5
_sas_det_pixsiz_x 0.01
_sas_det_pixsiz_y 0.01
_sas_det_center_x 2.0
_sas_det_center_y 2.2
_sas_det_sector_width 45
_sas_det_sector_orientation 22.5
_diffrn_ambient_temperature 277
_diffrn_ambient_environment air
_sas_sample_name
; Chicken egg white lysozyme in solution
;
_sas_sample_concentration 15
_sas_sample_buffer_composition "150mM NaCl, 40 mM Na acetate"
_sas_sample_buffer_pH 4.25
_sas_sample_thickness 0.2
_sas_sample_transmission 0.6
_sas_sample_exposure_time 600
_sas_trt_detres_made Yes
_sas_trt_matrix_made Yes
_sas_trt_background_made Yes
_sas_trt_date 07-Jul-1997
_sas_block_data_id "07-09-98 02:46am|Exa_for_sasCIF|Diff"
_sas_data_type Sample
_sas_data_title "Lysozyme difference data"
_sas_data_momentum_factor 0.62831
_sas_data_scaling_factor 1e-6
loop_ _sas_data_momentum_transfer
_sas_data_intensity
_sas_data_stat_error
5.210180E-02 , 86.182260 , 6.284270
5.384985E-02 , 84.223050 , 5.760499
5.559791E-02 , 82.234630 , 5.395226
5.734596E-02 , 78.108730 , 5.148366
5.909401E-02 , 77.326730 , 4.874490
# ..... truncated for brievity
5.258238E-01 , 5.752596 , 6.161484E-01
5.275719E-01 , 4.321647 , 6.167618E-01
5.293199E-01 , 5.015543 , 6.191652E-01
5.310680E-01 , 5.677856 , 6.121474E-01
5.328161E-01 , 5.151685 , 6.183262E-01
# The file may contain other data sets (matrix scattering,
# another sampls(s), detector response etc) identified by their
# own _sas_block_data_id
#--eof--eof--eof--eof--eof--eof--eof--eof--eof--eof--eof--eof--eof
##############################################################################
# #
# SAS CIF Dictionary #
# --------------------- #
# #
# CIF data definitions specifically for SAS applications. #
# These are in addition to those defined in the Core CIF Dictionary 1996. #
# #
# The DDL commands used in this dictionary are defined in "ddl_core.dic". #
# #
##############################################################################
data_on_this_dictionary
_dictionary_name cif_sas.dic
_dictionary_version 0.1
_dictionary_update 1998-08-17
_dictionary_history
;
1998-08-17 Initial definitions
;
#......................... Block/Dataset names
data_sas_block_data_[sas]
_name '_sas_block_data_[sas]'
_category category_overview
_type null
#.............................................................
data_sas_block_data_id
_name '_sas_block_data_id'
_category sas_block
_type char
_definition
; It is used to assign an unique id code
to a data block.
;
#......................... Beam Information
data_sas_beam_[sas]
_name '_sas_beam_[sas]'
_category category_overview
_type null
#.............................................................
data_sas_beam_collimation_slit_
loop_ _name '_sas_beam_collimation_slit_x'
'_sas_beam_collimation_slit_y'
_category sas_beam
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_list both
_definition
; defines the collimation slits in the equatorial
and axial direction.
;
data_sas_beam_size_
loop_ _name '_sas_beam_size_x'
'_sas_beam_size_y'
_category sas_beam
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_list both
_definition
; defines the beam size on the sample
;
data_sas_beam_divergence_
loop_ _name '_sas_beam_divergence_x'
'_sas_beam_divergence_y'
_category sas_beam
_type numb
_enumeration_range 0.0:
_units rad
_units_detail 'radians'
_list both
_definition
; defines the beam divergency
;
data_sas_beam_collimation_distance
_name '_sas_beam_collimation_distance'
_category sas_beam
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_definition
; defines the collimation distance
;
data_sas_beam_sample_detector
_name '_sas_beam_sample_detector'
_category sas_beam
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_definition
; defines the distance sample/detector
;
data_sas_beam_delta_lambda
_name '_sas_beam_delta_lambda'
_category sas_beam
_type numb
_enumeration_range 0.0:
_definition
; defines the quantity (Delta lambda ) / lambda
Lambda being the wavelength
;
#......................... Detector Information
data_sas_det_[sas]
_name '_sas_det_[sas]'
_category category_overview
_type null
#.............................................................
data_sas_det_beamstop_
loop_ _name '_sas_det_beamstop_x'
'_sas_det_beamstop_y'
_category sas_det
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_list both
_definition
; defines the beamstop size.
;
data_sas_det_pixnum_
loop_ _name '_sas_det_pixnum_x'
'_sas_det_pixnum_y'
_category sas_det
_type numb
_enumeration_range 0.0:
_list both
_definition
; defines the number of detector pixel
in x and y direction.
;
data_sas_det_pixsize_
loop_ _name '_sas_det_pixsize_x'
'_sas_det_pixsize_y'
_category sas_det
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_list both
_definition
; defines the pixel size in x and y direction.
;
data_sas_det_center_
loop_ _name '_sas_det_center_x'
'_sas_det_center_y'
_category sas_det
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_list both
_definition
; defines the beam center on the detector in
x and y directions.
The X coordinate is defined from left and
the Y coordinate is defined from bottom.
;
data_sas_det_rad_step
_name '_sas_det_rad_step'
_category sas_det
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_definition
; defines the radial step to group pixels for
circular average.
;
data_sas_det_mer_fact
_name '_sas_det_mer_fact'
_category sas_det
_type numb
_enumeration_range 0.0:
_definition
; defines the number of channels merged
together for the 1D-detector
;
data_sas_det_rotation
_name '_sas_det_rotation'
_category sas_det
_type numb
_enumeration_range -180.0:360.0
_units deg
_units_detail 'degrees'
_definition
; defines the tilt of the detector
;
data_sas_det_sector_
loop_ _name '_sas_det_sector_width'
'_sas_det_sector_orientation'
_category sas_det
_type numb
_enumeration_range -180.0:360.0
_units deg
_units_detail 'degrees'
_list both
_definition
; defines the sector width for sectorial average
and the sector orientation with respect
x direction.
;
#......................... Sample Information
data_sas_sample_[sas]
_name '_sas_sample_[sas]'
_category category_overview
_type null
#.............................................................
data_sas_sample_name
_name '_sas_sample_name'
_category sas_sample
_type char
_definition
;
A description of the specimen such as the source of the specimen,
identification of standards, mixtures, etc.
;
data_sas_sample_concentration
_name '_sas_sample_concentration'
_category sas_sample
_type numb
_enumeration_range 0.0:
_units gl-1
_units_detail 'gramme/liter'
_definition
;
The sample concentration.
;
data_sas_sample_thickness
_name '_sas_sample_thickness'
_category sas_sample
_type numb
_enumeration_range 0.0:
_units cm
_units_detail 'centimeters'
_definition
;
The sample thickness
;
data_sas_sample_transmission
_name '_sas_sample_transmission'
_category sas_sample
_type numb
_enumeration_range 0.0:
_definition
;
The sample transmission
;
data_sas_sample_time
_name '_sas_sample_time'
_category sas_sample
_type numb
_enumeration_range 0.0:
_units s
_units_detail 'seconds'
_definition
;
A description of the sample in case of kinematic
measurments.
;
data_sas_sample_strain
_name '_sas_sample_strain'
_category sas_sample
_type numb
_enumeration_range 0.0:
_definition
;
The sample strain
;
data_sas_sample_pressure
_name '_sas_sample_pressure'
_category sas_sample
_type numb
_enumeration_range 0.0:
_units Pa
_units_detail 'Pascals'
_definition
;
The sample pressure
;
data_sas_sample_orientation
_name '_sas_sample_orientation'
_category sas_sample
_type numb
_enumeration_range -180.0:360.0
_units deg
_units_detail 'degrees'
_definition
;
defines the angle between the sample normal and
the incident beam.
;
data_sas_sample_monitor
_name '_sas_sample_monitor'
_category sas_sample
_type numb
_enumeration_range 0.0:
_definition
;
Sample calibration channel value
;
data_sas_sample_buffer_composition
_name '_sas_sample_buffer_composition'
_category sas_sample
_type char
_definition
; A description of the buffer used
;
data_sas_sample_buffer_ph
_name '_sas_sample_buffer_ph'
_category sas_sample
_type numb
_enumeration_range 0.0:14.0
_definition
;
Buffer ph
;
data_sas_sample_matrix_monitor
_name '_sas_sample_matrix_monitor'
_category sas_sample
_type numb
_definition
;
Matrix callibration channel value
;
data_sas_sample_exposure
_name '_sas_sample_exposure'
_category sas_sample
_type numb
_enumeration_range 0.0:
_units s
_units_detail 'seconds'
_definition
;
Exposure time of the sample
;
#......................... Treatment Information
data_sas_trt_[sas]
_name '_sas_trt_[sas]'
_category category_overview
_type null
#.............................................................
data_sas_trt_detrep_made
_name '_sas_trt_detrep_made'
_category sas_trt
_type char
loop_ _enumeration yes
no
_definition
;
Data normalized against response
;
data_sas_trt_detrep_block
_name '_sas_trt_detrep_block'
_category sas_trt
_type char
_definition
;
Detector response data block
;
data_sas_trt_matrix_made
_name '_sas_trt_matrix_made'
_category sas_trt
_type char
loop_ _enumeration yes
no
_definition
;
Matrix/buffer scattering subtracted
;
data_sas_trt_matrix_block
_name '_sas_trt_matrix_block'
_category sas_trt
_type char
_definition
;
Matrix/buffer scattering block
;
data_sas_trt_matrix_transmission
_name '_sas_trt_matrix_transmission'
_category sas_trt
_type numb
_enumeration_range 0.0:
_definition
;
The matrix transmission
;
data_sas_trt_background_made
_name '_sas_trt_background_made'
_category sas_trt
_type char
loop_ _enumeration yes
no
_definition
;
Background subtracted
;
data_sas_trt_background_block
_name '_sas_trt_background_block'
_category sas_trt
_type char
_definition
;
Background scattering block
;
data_sas_trt_background_transmission
_name '_sas_trt_background_transmission'
_category sas_trt
_type numb
_enumeration_range 0.0:
_definition
;
The transmission of empty cell
;
data_sas_trt_raw_data_file
_name '_sas_trt_raw_data_file'
_category sas_trt
_type char
_definition
;
Acquisition data file
;
data_sas_trt_raw_data_date
_name '_sas_trt_raw_data_date'
_category sas_trt
_type char
_definition
;
Date and time of raw data file acquisition.
Dates and times should be specified in the standard
CIF format 'yyyy-mm-ddThh:mm:ss+zz'. Use of seconds
and a time zone is optional, but use of hours and minutes
is strongly encouraged.
;
data_sas_trt_date
_name '_sas_trt_date'
_category sas_trt
_type char
_definition
;
Date and time of traetment
Dates and times should be specified in the standard
CIF format 'yyyy-mm-ddThh:mm:ss+zz'. Use of seconds
and a time zone is optional, but use of hours and minutes
is strongly encouraged.
;
#......................... Data Information
data_sas_data_[sas]
_name '_sas_data_[sas]'
_category category_overview
_type null
#.............................................................
data_sas_data_type
_name '_sas_data_type'
_category sas_data
_type char
loop_ _enumeration sample
matrix
background
detector
_definition
;
data type
;
data_sas_data_title
_name '_sas_data_title'
_category sas_data
_type char
_definition
;
data title
;
data_sas_data_momentum_transfert
_name '_sas_data_momentum_transfert'
_category sas_data
_type numb
_list yes
_definition
;
Momentum transfert values
;
data_sas_data_momentum_factor
_name '_sas_data_momentum_factor'
_category sas_data
_type numb
_definition
;
Scaling factor of the momentum transfert to
4*PI sin (theta) / lambda in A-1
;
data_sas_data_intensity
_name '_sas_data_intensity'
_category sas_data
_type numb
_list yes
_definition
;
Scattering intensity
;
data_sas_data_stat_error
_name '_sas_data_stat_error'
_category sas_data
_type numb
_list yes
_definition
;
Statistical errors associated to the scattering intensity
;
data_sas_data_sys_error
_name '_sas_data_sys_error'
_category sas_data
_type numb
_list yes
_definition
;
Systematic errors, e.g. from radial average etc...
;
data_sas_data_scaling_factor
_name '_sas_data_scaling_factor'
_category sas_data
_type numb
_definition
;
Scaling factor for the intensity and errors.
;
data_sas_data_group_factor
_name '_sas_data_group_factor'
_category sas_data
_type numb
_list yes
_definition
;
Number of pixels contributing to this point.
;
data_sas_data_resolution
_name '_sas_data_resolution'
_category sas_data
_type numb
_list yes
_definition
;
Width of Gaussian resolution function.
;
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