CBFlib
An API for CBF/imgCIF
Crystallographic Binary Files with ASCII Support
Version 0.9.2
12 February 2011
by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory
and
Herbert J. Bernstein
Bernstein + Sons
yaya at bernstein-plus-sons dot com
(c) Copyright 2006, 2007, 2008, 2011 Herbert J. Bernstein
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YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL.
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF THE
LGPL.
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Before using this software, please read the
NOTICE
for important disclaimers and the IUCr Policy on the Use of the Crystallographic
Information File (CIF) and for other important information.
Work on imgCIF and CBFlib supported in part by the U. S. Department of
Energy (DOE) under grants ER63601-1021466-0009501 and
ER64212-1027708-0011962, by the U. S. National Science Foundation (NSF)
under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S. National
Institutes of Health (NIH) under grants 1R15GM078077 from NIGMS and
1R13RR023192 from NCRR and funding from the International Union for
Crystallographyn (IUCr). The content is solely the responsibility of the
authors and does not necessarily represent the official views of DOE, NSF,
NIH, NIGMS, NCRR or IUCr.
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Version History
Version Date By Description
0.1 Apr. 1998 PJE This was the first CBFlib release.
It supported binary CBF files using
binary strings.
0.2 Aug. 1998 HJB This release added ascii imgCIF
support using MIME-encoded binary
sections, added the option of MIME
headers for the binary strings was
well. MIME code adapted from mpack
1.5. Added hooks needed for DDL1-style
names without categories.
0.3 Sep. 1998 PJE This release cleaned up the changes
made for version 0.2, allowing
multi-threaded use of the code, and
removing dependence on the mpack
package.
0.4 Nov. 1998 HJB This release merged much of the
message digest code into the general
file reading and writing to reduce the
number of passes. More consistency
checking between the MIME header and
the binary header was introduced. The
size in the MIME header was adjusted
to agree with the version 0.2
documentation.
0.5 Dec. 1998 PJE This release greatly increased the
speed of processing by allowing for
deferred digest evaluation.
0.6 Jan. 1999 HJB This release removed the redundant
information (binary id, size,
compression id) from a binary header
when there is a MIME header, removed
the unused repeat argument, and made
the memory allocation for buffering
and tables with many rows sensitive to
the current memory allocation already
used.
0.6.1 Feb. 2001 HP (per This release fixed a memory leak due
HJB) to misallocation by size of cbf_handle
instead of cbf_handle_struct
0.7 Mar. 2001 PJE This release added high-level
instructions based on the imgCIF
dictionary version 1.1.
0.7.1 Mar. 2001 PJE The high-level functions were
revised to permit future expansion to
files with multiple images.
0.7.2 Apr. 2001 HJB This release adjusted cbf_cimple.c
to conform to cif_img.dic version
1.1.3
0.7.2.1 May 2001 PJE This release corrected an if nesting
error in the prior mod to
cbf_cimple.c.
0.7.3 Oct. 2002 PJE This release modified cbf_simple.c
to reorder image data on read so that
the indices are always increasing in
memory (this behavior was undefined
previously).
0.7.4 Jan 2004 HJB This release fixes a parse error for
quoted strings, adds code to get and
set character string types, and
removes compiler warnings
0.7.5 Apr 2006 HJB This release cleans up some compiler
warnings, corrects a parse error on
quoted strings with a leading blank as
adds the new routines for support of
aliases, dictionaries and real arrays,
higher level routines to get and set
pixel sizes, do cell computations, and
to set beam centers, improves support
for conversion of images, picking up
more data from headers.
0.7.6 Jul 2006 HJB This release reorganizes the kit
into two pieces:
CBFlib_0.7.6_Data_Files and
CBFlib_0.7.6. An optional local copy
of getopt is added. The 1.4 draft
dictionary has been added. cif2cbf
updated to support vcif2 validation.
convert_image and cif2cbf updated to
report text of error messages.
convert_image updated to support tag
and category aliases, default to adxv
images. convert_image and img updated
to support row-major images. Support
added for binning. API Support added
for validation, wide files and line
folding. Logic changed for beam center
reporting. Added new routines:
cbf_validate, cbf_get_bin_sizes,
cbf_set_bin_sizes,
cbf_find_last_typed_child,
cbf_compose_itemname,
cbf_set_cbf_logfile,
cbf_make_widefile, cbf_read_anyfile,
cbf_read_widefile,
cbf_write_local_file,
cbf_write_widefile, cbf_column_number,
cbf_blockitem_number, cbf_log,
cbf_check_category_tags,
cbf_set_beam_center
0.7.7 February 2007 HJB This release reflects changes for
base 32K support developed by G.
Darakev, and changes for support of
reals, 3d arrays, byte_offset
compression and J. P. Abrahams packed
compression made in consultation with
(in alphabetic order) E. Eikenberry,
A. Hammerley, W. Kabsch, M. Kobas, J.
Wright and others at PSI and ESRF in
January 2007, as well accumulated
changes fixing problems in release
0.7.6.
0.7.7.1 February 2007 HJB This release is a patch to 0.7.7 to
change the treatment of the byteorder
parameter from strcpy semantics to
return of a pointer to a string
constant. Our thanks to E. Eikenberry
for pointing out the problem.
0.7.7.2 February 2007 HJB This release is a patch to 0.7.7.1
to add testing for JPA packed
compression and to respect signs
declared in the MIME header.
0.7.7.3 April 2007 HJB This release is a patch to 0.7.7.3
to add f90 support for reading of CBF
byte-offset and packed compression, to
fix problems with gcc 4.4.1 and to
correct errors in multidimensional
packed compression.
0.7.7.4 May 2007 HJB Corrects in handling SLS detector
mincbfs and reorder dimensions versus
arrays for some f90 compilers as per
H. Powell.
0.7.7.5 May 2007 HJB Fix to cbf_get_image for bug
reported by F. Remacle, fixes for
windows builds as per J. Wright and F.
Remacle.
0.7.7.6 Jun 2007 HJB Fix to CBF byte-offset compression
writes, fix to Makefiles and m4 for
f90 test programs to allow adjustable
record length.
0.7.8 Jul 2007 HJB Release for full support of SLS data
files with updated convert_minicbf,
and support for gfortran from gcc 4.2.
0.7.8.1 Jul 2007 HJB Update to 0.7.8 release to fix
memory leaks reported by N. Sauter and
to update validation checks for recent
changes.
0.7.8.2 Dec 2007 CN, HJB Update to 0.7.8.1 to add ADSC jiffie
by Chris Nielsen, and to add ..._fs
and ..._sf macros.
0.7.9 Dec 2007 CN, HJB Identical to 0.7.8.2 except for a
cleanup of deprecated examples, e.g.
diffrn_frame_data
0.7.9.1 Jan 2008 CN, HJB Update to 0.7.8.2 to add inverse
ADSC jiffie by Chris Nielsen, to clean
up problems in handling maps for
RasMol.
0.8.0 Jul 2008 GT, HJB Cleanup of 0.7.9.1 to start 0.8
series.
0.8.1 Jul 2009 EZ, CN, Release with EZ's 2008 DDLm support
PC, GW, using JH's PyCifRW, also cbff f95
JH, HJB wrapper code, PC's java bindings.
0.9.1 Aug 2010 PC, EE, Release with EE's Dectris template
JLM, NS, software, also with vcif3, new
EZ, HJB arvai_test, sequence_match.
0.9.2 Feb 2011 PC, EE, New default release with updated
JLM, NS, pycbf, tiff support, removal of
EZ, HJB default use of PyCifRW to avoid Fedora
license issue.
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Known Problems
The example program tiff2cbf needs the enviroment variable LD_LIBRARY_PATH
set to the location of the lib directory in CBFlib_0.9.2, unless a system
install of tiff-3.9.4-rev-6Feb11 has been done.
Due to license issues, PyCifRW is not included with default releases of
CBFlib. Users can download PyCifRW separately.
There are some issues with Peter Chang's lastest java wrapper under the
CBFlib 0.9.2 release. Until they are resolved, the CBFlib 0.8.1 release
should be used for Java applications.
This version does not have support for predictor compression.
Code is needed to support array sub-sections.
Foreword
In order to work with CBFlib, you need:
* the source code, in the form of a "gzipped" tar, CBFlib_0.9.2.tar.gz;
and
* the test data:
* CBFlib_0.9.2_Data_Files_Input.tar.gz (17 MB) a "gzipped" tar of
the input data files needed to test the API;
* CBFlib_0.9.2_Data_Files_Output.tar.gz (36 MB) a "gzipped" tar of
the output data files needed to test the API, or, if space is at
a premium;
* CBFlib_0.9.2_Data_Files_Output_Sigs_Only.tar.gz (1 KB) is a
"gzipped" tar of only the MD5 signatures of the output data files
needed to test the API.
If your system has the program wget, you only need the source code. The
download of the other tar balls will be handled automatically.
Be careful about space. A full build and test can use 350 MB or more. If
space is tight, be sure to read the instructions below on using only the
signatures of the test files.
Uncompress and unpack :
* gunzip < CBFlib_0.9.2.tar.gz | tar xvf -
To run the test programs, you will also need Paul Ellis's sample MAR345
image, example.mar2300, Chris Nielsen's sample ADSC Quantum 315 image,
mb_LP_1_001.img, and Eric Eikenberry's SLS sample Pilatus 6m image,
insulin_pilatus6m, as sample data. In addition there are is a PDB mmCIF
file, 9ins.cif, and 3 special test files testflatin.cbf,
testflatpackedin.cbf and testrealin.cbf. All these files will be dowloaded
and extracted by the Makefile from CBFlib_0.9.2_Data_Files_Input. Do not
download copies into the top level directory.
Thare are various sample Makefiles for common configurations. The
Makefile_OSX samples is for systems with gfortran from prior to the
release of gcc 4.2. For the most recent gfortran, use Makefile_OSX_gcc42.
All the Makefiles are generated from m4/Makefile.m4.
The Makefiles use GNU make constructs, such as ifeq and ifneq. If you need
to use a different version of make, you will need to edit out the
conditionals
The operation of the Makefiles is sensitive to the following environment
variables:
* CBFLIB_USE_PYCIFRW If you define this environment variable, you may
rebuild the Makefiles to include James Hester's PyCifRW. The process
under bash is:
export CBFLIB_USE_PYCIFRW=yes
cd CBFlib_0.9.2
touch m4/Makefile.m4
make Makefiles
* CBF_DONT_USE_LONG_LONG If you define this environment variable, use of
the long long data type in CBFlib is replaced by use of a struct. The
Makefiles do not need to be rebuilt. Makefile_MINGW does not use the
long long data type even without defining this variable.
* NOFORTRAN If you define this environment variable, use of the fortran
compiler is suppressed.
If necessary, adjust the definition of CC and C++ and other defintions in
Makefile to point to your compilers. Set the definition of CFLAGS to an
appropriate value for your C and C++ compilers, the definition of F90C to
point to your Fortan-90/95 compiler, and the definitions of F90FLAGS and
F90LDFLAGS to approriate values for your Fortan-90/95 compilers, and then
make all
make tests
or, if space is at a premium:
make all
make tests_sigs_only
If you do not have a fortran compiler, you will need edit the Makefile or
to define the variable NOFORTRAN, either in the Makefile or in the
environment
We have included examples of CBF/imgCIF files produced by CBFlib in the
test data CBFlib_0.9.2_Data_Files_Output.tar.gz, the current best draft of
the CBF Extensions Dictionary, and of Andy Hammersley's CBF definition,
updated to become a DRAFT CBF/ImgCIF DEFINITION.
CBFlib 0.9.2 includes a program, tiff2cbf, to convert from tiff files to
CBF files, that requires an augmented version of tiff-3.9.4 called
tiff-3.9.4-rev-6Feb11, that installs into the CBFlib_0.9.2 directory. If a
system copy is desired, download and install
http://downloads.sf.net/cbflib/tiff-3.9.4-rev-6Feb11.tar.gz
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Contents
* 1. Introduction
* 2. Function descriptions
* 2.1 General description
* 2.1.1 CBF handles
* 2.1.2 CBF goniometer handles
* 2.1.3 CBF detector handles
* 2.1.4 Return values
* 2.2 Reading and writing files containing binary sections
* 2.2.1 Reading binary sections
* 2.2.2 Writing binary sections
* 2.2.3 Summary of reading and writing files containing binary
sections
* 2.2.4 Ordering of array indices
* 2.3 Low-level function prototypes
* 2.3.1 cbf_make_handle
* 2.3.2 cbf_free_handle
* 2.3.3 cbf_read_file, cbf_read_widefile
* 2.3.4 cbf_write_file, cbf_write_widefile
* 2.3.5 cbf_new_datablock, cbf_new_saveframe
* 2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
* 2.3.7 cbf_new_category
* 2.3.8 cbf_force_new_category
* 2.3.9 cbf_new_column
* 2.3.10 cbf_new_row
* 2.3.11 cbf_insert_row
* 2.3.12 cbf_delete_row
* 2.3.13 cbf_set_datablockname, cbf_set_saveframename
* 2.3.14 cbf_reset_datablocks
* 2.3.15 cbf_reset_datablock, cbf_reset_saveframe
* 2.3.16 cbf_reset_category
* 2.3.17 cbf_remove_datablock, cbf_remove_saveframe
* 2.3.18 cbf_remove_category
* 2.3.19 cbf_remove_column
* 2.3.20 cbf_remove_row
* 2.3.21 cbf_rewind_datablock
* 2.3.22 cbf_rewind_category, cbf_rewind_saveframe,
cbf_rewind_blockitem
* 2.3.23 cbf_rewind_column
* 2.3.24 cbf_rewind_row
* 2.3.25 cbf_next_datablock
* 2.3.26 cbf_next_category, cbf_next_saveframe,
cbf_next_blockitem
* 2.3.27 cbf_next_column
* 2.3.28 cbf_next_row
* 2.3.29 cbf_find_datablock
* 2.3.30 cbf_find_category, cbf_find_saveframe,
cbf_find_blockitem
* 2.3.31 cbf_find_column
* 2.3.32 cbf_find_row
* 2.3.33 cbf_find_nextrow
* 2.3.34 cbf_count_datablocks
* 2.3.35 cbf_count_categories, cbf_count_saveframes,
cbf_count_blockitems
* 2.3.36 cbf_count_columns
* 2.3.37 cbf_count_rows
* 2.3.38 cbf_select_datablock
* 2.3.39 cbf_select_category, cbf_select_saveframe,
cbf_select_blockitem
* 2.3.40 cbf_select_column
* 2.3.41 cbf_select_row
* 2.3.42 cbf_datablock_name
* 2.3.43 cbf_category_name
* 2.3.44 cbf_column_name, cbf_set_column_name
* 2.3.45 cbf_row_number
* 2.3.46 cbf_get_value, cbf_require_value
* 2.3.47 cbf_set_value
* 2.3.48 cbf_get_typeofvalue
* 2.3.49 cbf_set_typeofvalue
* 2.3.50 cbf_get_integervalue, cbf_require_integervalue
* 2.3.51 cbf_set_integervalue
* 2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
* 2.3.53 cbf_set_doublevalue
* 2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims,
cbf_get_integerarrayparameters_wdims_fs,
cbf_get_integerarrayparameters_wdims_sf
cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims,
cbf_get_realarrayparameters_wdims_fs,
cbf_get_realarrayparameters_wdims_sf
* 2.3.55 cbf_get_integerarray, cbf_get_realarray
* 2.3.56 cbf_set_integerarray,
cbf_set_integerarray_wdims,
cbf_set_integerarray_wdims_fs,
cbf_set_integerarray_wdims_sf,
cbf_set_realarray,
cbf_set_realarray_wdims, cbf_set_realarray_wdims_fs,
cbf_set_realarray_wdims_sf
* 2.3.57 cbf_failnez
* 2.3.58 cbf_onfailnez
* 2.3.59 cbf_require_datablock
* 2.3.60 cbf_require_category
* 2.3.61 cbf_require_column
* 2.3.62 cbf_require_column_value
* 2.3.63 cbf_require_column_integervalue
* 2.3.64 cbf_require_column_doublevalue
* 2.3.65 cbf_get_local_integer_byte_order,
cbf_get_local_real_byte_order, cbf_get_local_real_format
* 2.3.66 cbf_get_dictionary, cbf_set_dictionary,
cbf_require_dictionary
* 2.3.67 cbf_convert_dictionary
* 2.3.68 cbf_find_tag, cbf_find_local_tag
* 2.3.69 cbf_find_category_root, cbf_set_category_root,
cbf_require_category_root
* 2.3.70 cbf_find_tag_root, cbf_set_tag_root,
cbf_require_tag_root
* 2.3.71 cbf_find_tag_category, cbf_set_tag_category
* 2.4 High-level function prototypes (new for version 0.7)
* 2.4.1 cbf_read_template
* 2.4.2 cbf_get_diffrn_id, cbf_require_diffrn_id
* 2.4.3 cbf_set_diffrn_id
* 2.4.4 cbf_get_crystal_id
* 2.4.5 cbf_set_crystal_id
* 2.4.6 cbf_get_wavelength
* 2.4.7 cbf_set_wavelength
* 2.4.8 cbf_get_polarization
* 2.4.9 cbf_set_polarization
* 2.4.10 cbf_get_divergence
* 2.4.11 cbf_set_divergence
* 2.4.12 cbf_count_elements
* 2.4.13 cbf_get_element_id
* 2.4.14 cbf_get_gain
* 2.4.15 cbf_set_gain
* 2.4.16 cbf_get_overload
* 2.4.17 cbf_set_overload
* 2.4.18 cbf_get_integration_time
* 2.4.19 cbf_set_integration_time
* 2.4.20 cbf_get_time
* 2.4.21 cbf_set_time
* 2.4.22 cbf_get_date
* 2.4.23 cbf_set_date
* 2.4.24 cbf_set_current_time
* 2.4.25 cbf_get_image_size, cbf_get_image_size_fs,
cbf_get_image_size_fs,
cbf_get_3d_image_size, cbf_get_3d_image_size_fs,
cbf_get_3d_image_size_sf
* 2.4.26 cbf_get_image, cbf_get_image_fs, cbf_get_image_sf,
cbf_get_real_image, cbf_get_real_image_fs,
cbf_get_real_image_sf,
cbf_get_3d_image, cbf_get_3d_image_fs,
cbf_get_3d_image_sf,
cbf_get_real_3d_image, cbf_get_real_3d_image_fs,
cbf_get_real_3d_image_sf
* 2.4.27 cbf_set_image, cbf_set_image_fs, cbf_set_image_sf,
cbf_set_real_image, cbf_set_real_image_fs,
cbf_set_real_image_sf,
cbf_set_3d_image, cbf_set_3d_image, cbf_set_3d_image,
cbf_set_real_3d_image, cbf_set_real_3d_image_fs,
cbf_set_real_3d_image_sf
* 2.4.28 cbf_get_axis_setting
* 2.4.29 cbf_set_axis_setting
* 2.4.30 cbf_construct_goniometer
* 2.4.31 cbf_free_goniometer
* 2.4.32 cbf_get_rotation_axis
* 2.4.33 cbf_get_rotation_range
* 2.4.34 cbf_rotate_vector
* 2.4.35 cbf_get_reciprocal
* 2.4.36 cbf_construct_detector,
cbf_construct_reference_detector,
cbf_require_reference_detector
* 2.4.37 cbf_free_detector
* 2.4.38 cbf_get_beam_center, cbf_get_beam_center_fs,
cbf_get_beam_center_sf,
cbf_set_beam_center, cbf_set_beam_center_fs,
cbf_set_beam_center_sf,
cbf_set_reference_beam_center,
cbf_set_reference_beam_center_fs,
cbf_set_reference_beam_center_sf
* 2.4.39 cbf_get_detector_distance
* 2.4.40 cbf_get_detector_normal
* 2.4.41 cbf_get_detector_axis_slow,
cbf_get_detector_axis_fast, cbf_get_detector_axes,
cbf_get_detector_axes_fs, cbf_get_detector_axes_sf
* 2.4.42 cbf_get_pixel_coordinates,
cbf_get_pixel_coordinates_fs, cbf_get_pixel_coordinates_sf
* 2.4.43 cbf_get_pixel_normal, cbf_get_pixel_normal_fs,
cbf_get_pixel_normal_sf
* 2.4.44 cbf_get_pixel_area, cbf_get_pixel_area_fs,
cbf_get_pixel_area_sf
* 2.4.45 cbf_get_pixel_size, cbf_get_pixel_size_fs,
cbf_get_pixel_size_sf
* 2.4.46 cbf_set_pixel_size, cbf_set_pixel_size_fs,
cbf_set_pixel_size_sf
* 2.4.47 cbf_get_inferred_pixel_size,
cbf_get_inferred_pixel_size_fs,
cbf_get_inferred_pixel_size_sf
* 2.4.48 cbf_get_unit_cell
* 2.4.49 cbf_set_unit_cell
* 2.4.50 cbf_get_reciprocal_cell
* 2.4.51 cbf_set_reciprocal_cell
* 2.4.52 cbf_compute_cell_volume
* 2.4.53 cbf_compute_reciprocal_cell
* 2.4.54 cbf_get_orientation_matrix,
cbf_set_orientation_matrix
* 2.4.55 cbf_get_bin_sizes, cbf_set_bin_sizes
* 2.5 F90 function interfaces
* 2.5.1 FCB_ATOL_WCNT
* 2.5.2 FCB_CI_STRNCMPARR
* 2.5.3 FCB_EXIT_BINARY
* 2.5.4 FCB_NBLEN_ARRAY
* 2.5.5 FCB_NEXT_BINARY
* 2.5.6 FCB_OPEN_CIFIN
* 2.5.7 FCB_PACKED: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
* 2.5.8 FCB_READ_BITS
* 2.5.9 FCB_READ_BYTE
* 2.5.10 FCB_READ_IMAGE_I2, FCB_READ_IMAGE_I4,
FCB_READ_IMAGE_3D_I2, FCB_READ_IMAGE_3D_I4
* 2.5.11 FCB_READ_LINE
* 2.5.12 FCB_READ_XDS_I2
* 2.5.13 FCB_SKIP_WHITESPACE
* 3. File format
* 3.1 General description
* 3.2 Format of the binary sections
* 3.2.1 Format of imgCIF binary sections
* 3.2.2 Format of CBF binary sections
* 3.3 Compression schemes
* 3.3.1 Canonical-code compression
* 3.3.2 CCP4-style compression
* 3.3.3 Byte_offset compression
* 4. Installation
* 5. Example programs
1. Introduction
CBFlib (Crystallographic Binary File library) is a library of ANSI-C
functions providing a simple mechanism for accessing Crystallographic
Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The
CBFlib API is loosely based on the CIFPARSE API for mmCIF files. Like
CIFPARSE, CBFlib does not perform any semantic integrity checks; rather it
simply provides functions to create, read, modify and write CBF binary
data files and imgCIF ASCII data files.
Starting with version 0.7.7, an envolving FCBlib (Fortran Crystallographic
Binary library) has been added. As of this release it includes code for
reading byte-offset and packed compression image files created by CBFlib.
2. Function descriptions
2.1 General description
Almost all of the CBFlib functions receive a value of type cbf_handle (a
CBF handle) as the first argument. Several of the high-level CBFlib
functions dealing with geometry receive a value of type cbf_goniometer (a
handle for a CBF goniometer object) or cbf_detector (a handle for a CBF
detector object).
All functions return an integer equal to 0 for success or an error code
for failure.
2.1.1 CBF handles
CBFlib permits a program to use multiple CBF objects simultaneously. To
identify the CBF object on which a function will operate, CBFlib uses a
value of type cbf_handle.
All functions in the library except cbf_make_handle expect a value of type
cbf_handle as the first argument.
The function cbf_make_handle creates and initializes a new CBF handle.
The function cbf_free_handle destroys a handle and frees all memory
associated with the corresponding CBF object.
2.1.2 CBF goniometer handles
To represent the goniometer used to orient a sample, CBFlib uses a value
of type cbf_goniometer.
A goniometer object is created and initialized from a CBF object using the
function cbf_construct_goniometer.
The function cbf_free_goniometer destroys a goniometer handle and frees
all memory associated with the corresponding object.
2.1.3 CBF detector handles
To represent a detector surface mounted on a positioning system, CBFlib
uses a value of type cbf_detector.
A goniometer object is created and initialized from a CBF object using one
of the functions cbf_construct_detector, cbf_construct_reference_detector
or cbf_require_reference_detector.
The function cbf_free_detector destroys a detector handle and frees all
memory associated with the corresponding object.
2.1.4 Return values
All of the CBFlib functions return 0 on success and an error code on
failure. The error codes are:
CBF_FORMAT The file format is invalid
CBF_ALLOC Memory allocation failed
CBF_ARGUMENT Invalid function argument
CBF_ASCII The value is ASCII (not binary)
CBF_BINARY The value is binary (not ASCII)
CBF_BITCOUNT The expected number of bits does
not match the actual number written
CBF_ENDOFDATA The end of the data was reached
before the end of the array
CBF_FILECLOSE File close error
CBF_FILEOPEN File open error
CBF_FILEREAD File read error
CBF_FILESEEK File seek error
CBF_FILETELL File tell error
CBF_FILEWRITE File write error
CBF_IDENTICAL A data block with the new name
already exists
CBF_NOTFOUND The data block, category, column or
row does not exist
CBF_OVERFLOW The number read cannot fit into the
destination argument. The destination has
been set to the nearest value.
CBF_UNDEFINED The requested number is not defined (e.g. 0/0; new for
version 0.7).
CBF_NOTIMPLEMENTED The requested functionality is not yet implemented (New
for version 0.7).
If more than one error has occurred, the error code is the logical OR of
the individual error codes.
2.2 Reading and writing files containing binary sections
2.2.1 Reading binary sections
The current version of CBFlib only decompresses a binary section from disk
when requested by the program.
When a file containing one or more binary sections is read, CBFlib saves
the file pointer and the position of the binary section within the file
and then jumps past the binary section. When the program attempts to
access the binary data, CBFlib sets the file position back to the start of
the binary section and then reads the data.
For this scheme to work:
1. The file must be a random-access file opened in binary mode (fopen ( ,"
rb")).
2. The program must not close the file. CBFlib will close the file using
fclose ( ) when it is no longer needed.
At present, this also means that a program cant read a file and then write
back to the same file. This restriction will be eliminated in a future
version.
When reading an imgCIF vs a CBF, the difference is detected automatically.
2.2.2 Writing binary sections
When a program passes CBFlib a binary value, the data is compressed to a
temporary file. If the CBF object is subsequently written to a file, the
data is simply copied from the temporary file to the output file.
The output file can be of any type. If the program indicates to CBFlib
that the file is a random-access and readable, CBFlib will conserve disk
space by closing the temporary file and using the output file as the
location at which the binary value is stored.
For this option to work:
1. The file must be a random-access file opened in binary update mode
(fopen ( , "w+b")).
2. The program must not close the file. CBFlib will close the file using
fclose ( ) when it is no longer needed.
If this option is not used:
1. CBFlib will continue using the temporary file.
2. CBFlib will not close the file. This is the responsibility of the main
program.
2.2.3 Summary of reading and writing files containing binary sections
1. Open disk files to read using the mode "rb".
2. If possible, open disk files to write using the mode "w+b" and tell
CBFlib that it can use the file as a buffer.
3. Do not close any files read by CBFlib or written by CBFlib with
buffering turned on.
4. Do not attempt to read from a file, then write to the same file.
2.2.4 Ordering of array indices
There are two major conventions in the ordering of array indices:
* fs: Fast to slow. The first array index (the one numbered "1") is the
one for which the values of that index change "fastest". That is, as
we move forward in memory, the value of this index changes more
rapidly than any other.
* sf: Slow to fast. The first array index (the one numbered "1") is the
one for which the values of that index change "slowest". That is as we
move forward in memory, the value of this index changes more slowly
than any other.
During the development of CBFlib, both conventions have been used. In
order to avoid confusion, the functions for which array indices are used
are available in three forms: a default version which may used either one
convention or the other, a form in which the name of the function has an
"_fs" suffix for the fast to slow convention and a form in which the name
of the function has a "_sf" suffix for the slow to fast convention.
Designers of applications are advised to use one of the two suffix
conventions. There is no burden on performance for using one convention or
the other. The differences are resolved at compile time by use of
preprocessor macros.
----------------------------------------------------------------------
----------------------------------------------------------------------
2.3 Low-level function prototypes
2.3.1 cbf_make_handle
PROTOTYPE
#include "cbf.h"
int cbf_make_handle (cbf_handle *handle);
DESCRIPTION
cbf_make_handle creates and initializes a new internal CBF object. All
other CBFlib functions operating on this object receive the CBF handle as
the first argument.
ARGUMENTS
handle Pointer to a CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.2 cbf_free_handle
----------------------------------------------------------------------
2.3.2 cbf_free_handle
PROTOTYPE
#include "cbf.h"
int cbf_free_handle (cbf_handle handle);
DESCRIPTION
cbf_free_handle destroys the CBF object specified by the handle and frees
all associated memory.
ARGUMENTS
handle CBF handle to free.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.1 cbf_make_handle
----------------------------------------------------------------------
2.3.3 cbf_read_file, cbf_read_widefile
PROTOTYPE
#include "cbf.h"
int cbf_read_file (cbf_handle handle, FILE *file, int flags);
int cbf_read_widefile (cbf_handle handle, FILE *file, int flags);
DESCRIPTION
cbf_read_file reads the CBF or CIF file file into the CBF object specified
by handle, using the CIF 1.0 convention of 80 character lines.
cbf_read_widefile reads the CBF or CIF file file into the CBF object
specified by handle, using the CIF 1.1 convention of 2048 character lines.
A warning is issued to stderr for ascii lines over the limit. No test is
performed on binary sections.
Validation is performed in three ways levels: during the lexical scan,
during the parse, and, if a dictionary was converted, against the value
types, value enumerations, categories and parent-child relationships
specified in the dictionary.
flags controls the interpretation of binary section headers, the parsing
of brackets constructs and the parsing of treble-quoted strings.
MSG_DIGEST: Instructs CBFlib to check that the digest of
the binary section matches any header digest
value. If the digests do not match, the call
will return CBF_FORMAT. This evaluation and
comparison is delayed (a "lazy" evaluation) to
ensure maximal processing efficiency. If an
immediately evaluation is required, see
MSG_DIGESTNOW, below.
MSG_DIGESTNOW: Instructs CBFlib to check that the digest of
the binary section matches any header digeste
value. If the digests do not match, the call
will return CBF_FORMAT. This evaluation and
comparison is performed during initial parsing
of the section to ensure timely error reporting
at the expense of processing efficiency. If a
more efficient delayed ("lazy") evaluation is
required, see MSG_DIGEST, above.
MSG_DIGESTWARN: Instructs CBFlib to check that the digest of
the binary section matches any header digeste
value. If the digests do not match, a warning
message will be sent to stderr, but processing
will attempt to continue. This evaluation and
comparison is first performed during initial
parsing of the section to ensure timely error
reporting at the expense of processing
efficiency. An mismatch of the message digest
usually indicates a serious error, but it is
sometimes worth continuing processing to try to
isolate the cause of the error. Use this option
with caution.
MSG_NODIGEST: Do not check the digest (default).
PARSE_BRACKETS: Accept DDLm bracket-delimited
[item,item,...item] or {item,item,...item} or
(item,item,...item) constructs as valid,
stripping non-quoted embedded whitespace and
comments. These constructs may span multiple
lines.
PARSE_LIBERAL_BRACKETS: Accept DDLm bracket-delimited
[item,item,...item] or {item,item,...item} or
(item,item,...item) constructs as valid,
stripping embedded non-quoted, non-separating
whitespace and comments. These constructs may
span multiple lines. In this case, whitespace
may be used as an alternative to the comma.
PARSE_TRIPLE_QUOTES: Accept DDLm triple-quoted
"""item,item,...item""" or
'''item,item,...item''' constructs as valid,
stripping embedded whitespace and comments.
These constructs may span multiple lines. If
this flag is set, then ''' will not be
interpreted as a quoted apoptrophe and """ will
not be interpreted as a quoted double quote mark
and
PARSE_NOBRACKETS: Do not accept DDLm bracket-delimited
[item,item,...item] or {item,item,...item} or
(item,item,...item) constructs as valid,
stripping non-quoted embedded whitespace and
comments. These constructs may span multiple
lines.
PARSE_NOTRIPLE_QUOTES: No not accept DDLm triple-quoted
"""item,item,...item""" or
'''item,item,...item''' constructs as valid,
stripping embedded whitespace and comments.
These constructs may span multiple lines. If
this flag is set, then ''' will be interpreted
as a quoted apostrophe and """ will be
interpreted as a quoted double quote mark.
CBFlib defers reading binary sections as long as possible. In the current
version of CBFlib, this means that:
1. The file must be a random-access file opened in binary mode (fopen ( ,
"rb")).
2. The program must not close the file. CBFlib will close the file using
fclose ( ) when it is no longer needed.
These restrictions may change in a future release.
ARGUMENTS
handle CBF handle.
file Pointer to a file descriptor.
headers Controls interprestation of binary section headers.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.4 cbf_write_file
----------------------------------------------------------------------
2.3.4 cbf_write_file
PROTOTYPE
#include "cbf.h"
int cbf_write_file (cbf_handle handle, FILE *file, int readable, int
ciforcbf, int flags, int encoding);
int cbf_write_widefile (cbf_handle handle, FILE *file, int readable, int
ciforcbf, int flags, int encoding);
DESCRIPTION
cbf_write_file writes the CBF object specified by handle into the file
file, following CIF 1.0 conventions of 80 character lines.
cbf_write_widefile writes the CBF object specified by handle into the file
file, following CIF 1.1 conventions of 2048 character lines. A warning is
issued to stderr for ascii lines over the limit, and an attempt is made to
fold lines to fit. No test is performed on binary sections.
If a dictionary has been provided, aliases will be applied on output.
Unlike cbf_read_file, the file does not have to be random-access.
If the file is random-access and readable, readable can be set to non-0 to
indicate to CBFlib that the file can be used as a buffer to conserve disk
space. If the file is not random-access or not readable, readable must be
0.
If readable is non-0, CBFlib will close the file when it is no longer
required, otherwise this is the responsibility of the program.
ciforcbf selects the format in which the binary sections are written:
CIF Write an imgCIF file.
CBF Write a CBF file (default).
flags selects the type of header used in CBF binary sections, selects
whether message digests are generated, and controls the style of output.
The value of flags can be a logical OR of any of:
MIME_HEADERS Use MIME-type headers (default).
MIME_NOHEADERS Use a simple ASCII headers.
MSG_DIGEST Generate message digests for binary data
validation.
MSG_NODIGEST Do not generate message digests (default).
PARSE_BRACKETS Do not convert bracketed strings to text fields
(default).
PARSE_LIBERAL_BRACKETS Do not convert bracketed strings to text fields
(default).
PARSE_NOBRACKETS Convert bracketed strings to text fields
(default).
PARSE_TRIPLE_QUOTES Do not convert triple-quoted strings to text
fields (default).
PARSE_NOTRIPLE_QUOTES Convert triple-quoted strings to text fields
(default).
PAD_1K Pad binary sections with 1023 nulls.
PAD_2K Pad binary sections with 2047 nulls.
PAD_4K Pad binary sections with 4095 nulls.
Note that on output, the types "prns&, "brcs" and "bkts" will be converted
to "text" fields if PARSE_NOBRACKETS has been set flags, and that the
types "tsqs" and "tdqs" will be converted to "text" fields if the flag
PARSE_NOTRIPLE_QUOTES has been set in the flags. It is an error to set
PARSE_NOBRACKETS and to set either PARSE_BRACKETS or
PARSE_LIBERAL_BRACKETS. It is an error to set both PARSE_NOTRIPLE_QUOTES
and PARSE_TRIPLE_QUOTES.
encoding selects the type of encoding used for binary sections and the
type of line-termination in imgCIF files. The value can be a logical OR of
any of:
ENC_BASE64 Use BASE64 encoding (default).
ENC_QP Use QUOTED-PRINTABLE encoding.
ENC_BASE8 Use BASE8 (octal) encoding.
ENC_BASE10 Use BASE10 (decimal) encoding.
ENC_BASE16 Use BASE16 (hexadecimal) encoding.
ENC_FORWARD For BASE8, BASE10 or BASE16 encoding, map bytes to words
forward (1234) (default on little-endian machines).
ENC_BACKWARD Map bytes to words backward (4321) (default on big-endian
machines).
ENC_CRTERM Terminate lines with CR.
ENC_LFTERM Terminate lines with LF (default).
ARGUMENTS
handle CBF handle.
file Pointer to a file descriptor.
readable If non-0: this file is random-access and readable and can be
used as a buffer.
ciforcbf Selects the format in which the binary sections are written
(CIF/CBF).
headers Selects the type of header in CBF binary sections and message
digest generation.
encoding Selects the type of encoding used for binary sections and the
type of line-termination in imgCIF files.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.3 cbf_read_file
----------------------------------------------------------------------
2.3.5 cbf_new_datablock, cbf_new_saveframe
PROTOTYPE
#include "cbf.h"
int cbf_new_datablock (cbf_handle handle, const char *datablockname);
int cbf_new_saveframe (cbf_handle handle, const char *saveframename);
DESCRIPTION
cbf_new_datablock creates a new data block with name datablockname and
makes it the current data block. cbf_new_saveframe creates a new save
frame with name saveframename within the current data block and makes the
new save frame the current save frame.
If a data block or save frame with this name already exists, the existing
data block or save frame becomes the current data block or save frame.
ARGUMENTS
handle CBF handle.
datablockname The name of the new data block.
saveframename The name of the new save frame.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.12 cbf_set_datablockname, cbf_set_saveframename
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
PROTOTYPE
#include "cbf.h"
int cbf_force_new_datablock (cbf_handle handle, const char
*datablockname);
int cbf_force_new_saveframe (cbf_handle handle, const char
*saveframename);
DESCRIPTION
cbf_force_new_datablock creates a new data block with name datablockname
and makes it the current data block. Duplicate data block names are
allowed. cbf_force_new_saveframe creates a new savew frame with name
saveframename and makes it the current save frame. Duplicate save frame
names are allowed.
Even if a save frame with this name already exists, a new save frame is
created and becomes the current save frame.
ARGUMENTS
handle CBF handle.
datablockname The name of the new data block.
saveframename The name of the new save frame.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.12 cbf_set_datablockname, cbf_set_saveframename
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.7 cbf_new_category
PROTOTYPE
#include "cbf.h"
int cbf_new_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_new_category creates a new category in the current data block with
name categoryname and makes it the current category.
If a category with this name already exists, the existing category becomes
the current category.
ARGUMENTS
handle CBF handle.
categoryname The name of the new category.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.18 cbf_remove_category
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.8 cbf_force_new_category
PROTOTYPE
#include "cbf.h"
int cbf_force_new_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_force_new_category creates a new category in the current data block
with name categoryname and makes it the current category. Duplicate
category names are allowed.
Even if a category with this name already exists, a new category of the
same name is created and becomes the current category. The allows for the
creation of unlooped tag/value lists drawn from the same category.
ARGUMENTS
handle CBF handle.
categoryname The name of the new category.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.18 cbf_remove_category
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.9 cbf_new_column
PROTOTYPE
#include "cbf.h"
int cbf_new_column (cbf_handle handle, const char *columnname);
DESCRIPTION
cbf_new_column creates a new column in the current category with name
columnname and makes it the current column.
If a column with this name already exists, the existing column becomes the
current category.
ARGUMENTS
handle CBF handle.
columnname The name of the new column.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.19 cbf_remove_column
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.10 cbf_new_row
PROTOTYPE
#include "cbf.h"
int cbf_new_row (cbf_handle handle);
DESCRIPTION
cbf_new_row adds a new row to the current category and makes it the
current row.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.11 cbf_insert_row
2.3.12 cbf_delete_row
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.11 cbf_insert_row
PROTOTYPE
#include "cbf.h"
int cbf_insert_row (cbf_handle handle, unsigned int rownumber);
DESCRIPTION
cbf_insert_row adds a new row to the current category. The new row is
inserted as row rownumber and existing rows starting from rownumber are
moved up by 1. The new row becomes the current row.
If the category has fewer than rownumber rows, the function returns
CBF_NOTFOUND.
The row numbers start from 0.
ARGUMENTS
handle CBF handle.
rownumber The row number of the new row.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.9 cbf_new_column
2.3.10 cbf_new_row
2.3.12 cbf_delete_row
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.12 cbf_delete_row
PROTOTYPE
#include "cbf.h"
int cbf_delete_row (cbf_handle handle, unsigned int rownumber);
DESCRIPTION
cbf_delete_row deletes a row from the current category. Rows starting from
rownumber +1 are moved down by 1. If the current row was higher than
rownumber, or if the current row is the last row, it will also move down
by 1.
The row numbers start from 0.
ARGUMENTS
handle CBF handle.
rownumber The number of the row to delete.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.18 cbf_remove_category
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.13 cbf_set_datablockname, cbf_set_saveframename
PROTOTYPE
#include "cbf.h"
int cbf_set_datablockname (cbf_handle handle, const char *datablockname);
int cbf_set_saveframename (cbf_handle handle, const char *saveframename);
DESCRIPTION
cbf_set_datablockname changes the name of the current data block to
datablockname. cbf_set_saveframename changes the name of the current save
frame to saveframename.
If a data block or save frame with this name already exists (comparison is
case-insensitive), the function returns CBF_IDENTICAL.
ARGUMENTS
handle CBF handle.
datablockname The new data block name.
datablockname The new save frame name.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.14 cbf_reset_datablocks
2.3.15 cbf_reset_datablock, cbf_reset_saveframe
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.42 cbf_datablock_name
----------------------------------------------------------------------
2.3.14 cbf_reset_datablocks
PROTOTYPE
#include "cbf.h"
int cbf_reset_datablocks (cbf_handle handle);
DESCRIPTION
cbf_reset_datablocks deletes all categories from all data blocks.
The current data block does not change.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.15 cbf_reset_datablock, cbf_reset_saveframe
2.3.18 cbf_remove_category
----------------------------------------------------------------------
2.3.15 cbf_reset_datablock, cbf_reset_datablock
PROTOTYPE
#include "cbf.h"
int cbf_reset_datablock (cbf_handle handle);
int cbf_reset_saveframe (cbf_handle handle);
DESCRIPTION
cbf_reset_datablock deletes all categories from the current data block.
cbf_reset_saveframe deletes all categories from the current save frame.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.14 cbf_reset_datablocks
2.3.18 cbf_remove_category
----------------------------------------------------------------------
2.3.16 cbf_reset_category
PROTOTYPE
#include "cbf.h"
int cbf_reset_category (cbf_handle handle);
DESCRIPTION
cbf_reset_category deletes all columns and rows from current category.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.16 cbf_reset_category
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
----------------------------------------------------------------------
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
PROTOTYPE
#include "cbf.h"
int cbf_remove_datablock (cbf_handle handle);
int cbf_remove_saveframe (cbf_handle handle);
DESCRIPTION
cbf_remove_datablock deletes the current data block. cbf_remove_saveframe
deletes the current save frame.
The current data block becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.5 cbf_new_datablock, cbf_new_saveframe
2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe
2.3.18 cbf_remove_category
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.18 cbf_remove_category
PROTOTYPE
#include "cbf.h"
int cbf_remove_category (cbf_handle handle);
DESCRIPTION
cbf_remove_category deletes the current category.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.7 cbf_new_category
2.3.8 cbf_force_new_category
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.19 cbf_remove_column
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.19 cbf_remove_column
PROTOTYPE
#include "cbf.h"
int cbf_remove_column (cbf_handle handle);
DESCRIPTION
cbf_remove_column deletes the current column.
The current column becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.9 cbf_new_column
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.18 cbf_remove_category
2.3.20 cbf_remove_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.20 cbf_remove_row
PROTOTYPE
#include "cbf.h"
int cbf_remove_row (cbf_handle handle);
DESCRIPTION
cbf_remove_row deletes the current row in the current category.
If the current row was the last row, it will move down by 1, otherwise, it
will remain the same.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.10 cbf_new_row
2.3.11 cbf_insert_row
2.3.17 cbf_remove_datablock, cbf_remove_saveframe
2.3.18 cbf_remove_category
2.3.19 cbf_remove_column
2.3.12 cbf_delete_row
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.21 cbf_rewind_datablock
PROTOTYPE
#include "cbf.h"
int cbf_rewind_datablock (cbf_handle handle);
DESCRIPTION
cbf_rewind_datablock makes the first data block the current data block.
If there are no data blocks, the function returns CBF_NOTFOUND.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.19 cbf_rewind_column
2.3.24 cbf_rewind_row
2.3.25 cbf_next_datablock
----------------------------------------------------------------------
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
PROTOTYPE
#include "cbf.h"
int cbf_rewind_category (cbf_handle handle);
int cbf_rewind_saveframe (cbf_handle handle);
int cbf_rewind_blockitem (cbf_handle handle, CBF_NODETYPE * type);
DESCRIPTION
cbf_rewind_category makes the first category in the current data block the
current category. cbf_rewind_saveframe makes the first saveframe in the
current data block the current saveframe. cbf_rewind_blockitem makes the
first blockitem (category or saveframe) in the current data block the
current blockitem. The type of the blockitem (CBF_CATEGORY or
CBF_SAVEFRAME) is returned in type.
If there are no categories, saveframes or blockitems the function returns
CBF_NOTFOUND.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
type CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.19 cbf_rewind_column
2.3.24 cbf_rewind_row
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
----------------------------------------------------------------------
2.3.23 cbf_rewind_column
PROTOTYPE
#include "cbf.h"
int cbf_rewind_column (cbf_handle handle);
DESCRIPTION
cbf_rewind_column makes the first column in the current category the
current column.
If there are no columns, the function returns CBF_NOTFOUND.
The current row is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.24 cbf_rewind_row
2.3.27 cbf_next_column
----------------------------------------------------------------------
2.3.24 cbf_rewind_row
PROTOTYPE
#include "cbf.h"
int cbf_rewind_row (cbf_handle handle);
DESCRIPTION
cbf_rewind_row makes the first row in the current category the current
row.
If there are no rows, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.19 cbf_rewind_column
2.3.28 cbf_next_row
----------------------------------------------------------------------
2.3.25 cbf_next_datablock
PROTOTYPE
#include "cbf.h"
int cbf_next_datablock (cbf_handle handle);
DESCRIPTION
cbf_next_datablock makes the data block following the current data block
the current data block.
If there are no more data blocks, the function returns CBF_NOTFOUND.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.27 cbf_next_column
2.3.28 cbf_next_row
----------------------------------------------------------------------
2.3.26 cbf_next_category
PROTOTYPE
#include "cbf.h"
int cbf_next_category (cbf_handle handle);
DESCRIPTION
cbf_next_category makes the category following the current category in the
current data block the current category.
If there are no more categories, the function returns CBF_NOTFOUND.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.25 cbf_next_datablock
2.3.27 cbf_next_column
2.3.27 cbf_next_row
----------------------------------------------------------------------
2.3.27 cbf_next_column
PROTOTYPE
#include "cbf.h"
int cbf_next_column (cbf_handle handle);
DESCRIPTION
cbf_next_column makes the column following the current column in the
current category the current column.
If there are no more columns, the function returns CBF_NOTFOUND.
The current row is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.19 cbf_rewind_column
2.3.25 cbf_next_datablock
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.28 cbf_next_row
----------------------------------------------------------------------
2.3.28 cbf_next_row
PROTOTYPE
#include "cbf.h"
int cbf_next_row (cbf_handle handle);
DESCRIPTION
cbf_next_row makes the row following the current row in the current
category the current row.
If there are no more rows, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.24 cbf_rewind_row
2.3.25 cbf_next_datablock
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.27 cbf_next_column
----------------------------------------------------------------------
2.3.29 cbf_find_datablock
PROTOTYPE
#include "cbf.h"
int cbf_find_datablock (cbf_handle handle, const char *datablockname);
DESCRIPTION
cbf_find_datablock makes the data block with name datablockname the
current data block.
The comparison is case-insensitive.
If the data block does not exist, the function returns CBF_NOTFOUND.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
datablockname The name of the data block to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.25 cbf_next_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.42 cbf_datablock_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.30 cbf_find_category
PROTOTYPE
#include "cbf.h"
int cbf_find_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_find_category makes the category in the current data block with name
categoryname the current category.
The comparison is case-insensitive.
If the category does not exist, the function returns CBF_NOTFOUND.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
categoryname The name of the category to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.29 cbf_find_datablock
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.43 cbf_category_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.31 cbf_find_column
PROTOTYPE
#include "cbf.h"
int cbf_find_column (cbf_handle handle, const char *columnname);
DESCRIPTION
cbf_find_column makes the columns in the current category with name
columnname the current column.
The comparison is case-insensitive.
If the column does not exist, the function returns CBF_NOTFOUND.
The current row is not affected.
ARGUMENTS
handle CBF handle.
columnname The name of column to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.19 cbf_rewind_column
2.3.27 cbf_next_column
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.32 cbf_find_row
2.3.44 cbf_column_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.32 cbf_find_row
PROTOTYPE
#include "cbf.h"
int cbf_find_row (cbf_handle handle, const char *value);
DESCRIPTION
cbf_find_row makes the first row in the current column with value value
the current row.
The comparison is case-sensitive.
If a matching row does not exist, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
value The value of the row to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.24 cbf_rewind_row
2.3.28 cbf_next_row
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.33 cbf_find_nextrow
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.33 cbf_find_nextrow
PROTOTYPE
#include "cbf.h"
int cbf_find_nextrow (cbf_handle handle, const char *value);
DESCRIPTION
cbf_find_nextrow makes the makes the next row in the current column with
value value the current row. The search starts from the row following the
last row found with cbf_find_row or cbf_find_nextrow, or from the current
row if the current row was defined using any other function.
The comparison is case-sensitive.
If no more matching rows exist, the function returns CBF_NOTFOUND.
The current column is not affected.
ARGUMENTS
handle CBF handle.
value the value to search for.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.24 cbf_rewind_row
2.3.28 cbf_next_row
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
----------------------------------------------------------------------
2.3.34 cbf_count_datablocks
PROTOTYPE
#include "cbf.h"
int cbf_count_datablocks (cbf_handle handle, unsigned int *datablocks);
DESCRIPTION
cbf_count_datablocks puts the number of data blocks in *datablocks .
ARGUMENTS
handle CBF handle.
datablocks Pointer to the destination data block count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.36 cbf_count_columns
2.3.37 cbf_count_rows
2.3.38 cbf_select_datablock
----------------------------------------------------------------------
2.3.35 cbf_count_categories
PROTOTYPE
#include "cbf.h"
int cbf_count_categories (cbf_handle handle, unsigned int *categories);
DESCRIPTION
cbf_count_categories puts the number of categories in the current data
block in *categories.
ARGUMENTS
handle CBF handle.
categories Pointer to the destination category count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.36 cbf_count_columns
2.3.37 cbf_count_rows
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
----------------------------------------------------------------------
2.3.36 cbf_count_columns
PROTOTYPE
#include "cbf.h"
int cbf_count_columns (cbf_handle handle, unsigned int *columns);
DESCRIPTION
cbf_count_columns puts the number of columns in the current category in
*columns.
ARGUMENTS
handle CBF handle.
columns Pointer to the destination column count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.37 cbf_count_rows
2.3.40 cbf_select_column
----------------------------------------------------------------------
2.3.37 cbf_count_rows
PROTOTYPE
#include "cbf.h"
int cbf_count_rows (cbf_handle handle, unsigned int *rows);
DESCRIPTION
cbf_count_rows puts the number of rows in the current category in *rows .
ARGUMENTS
handle CBF handle.
rows Pointer to the destination row count.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.36 cbf_count_columns
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.38 cbf_select_datablock
PROTOTYPE
#include "cbf.h"
int cbf_select_datablock (cbf_handle handle, unsigned int datablock);
DESCRIPTION
cbf_select_datablock selects data block number datablock as the current
data block.
The first data block is number 0.
If the data block does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
datablock Number of the data block to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.34 cbf_count_datablocks
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
2.3.40 cbf_select_column
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.39 cbf_select_category
PROTOTYPE
#include "cbf.h"
int cbf_select_category (cbf_handle handle, unsigned int category);
DESCRIPTION
cbf_select_category selects category number category in the current data
block as the current category.
The first category is number 0.
The current column and row become undefined.
If the category does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
category Number of the category to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems
2.3.38 cbf_select_datablock
2.3.40 cbf_select_column
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.40 cbf_select_column
PROTOTYPE
#include "cbf.h"
int cbf_select_column (cbf_handle handle, unsigned int column);
DESCRIPTION
cbf_select_column selects column number column in the current category as
the current column.
The first column is number 0.
The current row is not affected
If the column does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
column Number of the column to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.36 cbf_count_columns
2.3.38 cbf_select_datablock
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.41 cbf_select_row
PROTOTYPE
#include "cbf.h"
int cbf_select_row (cbf_handle handle, unsigned int row);
DESCRIPTION
cbf_select_row selects row number row in the current category as the
current row.
The first row is number 0.
The current column is not affected
If the row does not exist, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
row Number of the row to select.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.37 cbf_count_rows
2.3.38 cbf_select_datablock
2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem
2.3.40 cbf_select_column
----------------------------------------------------------------------
2.3.42 cbf_datablock_name
PROTOTYPE
#include "cbf.h"
int cbf_datablock_name (cbf_handle handle, const char **datablockname);
DESCRIPTION
cbf_datablock_name sets *datablockname to point to the name of the current
data block.
The data block name will be valid as long as the data block exists and has
not been renamed.
The name must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
datablockname Pointer to the destination data block name pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.29 cbf_find_datablock
----------------------------------------------------------------------
2.3.43 cbf_category_name
PROTOTYPE
#include "cbf.h"
int cbf_category_name (cbf_handle handle, const char **categoryname);
DESCRIPTION
cbf_category_name sets *categoryname to point to the name of the current
category of the current data block.
The category name will be valid as long as the category exists.
The name must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
categoryname Pointer to the destination category name pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
----------------------------------------------------------------------
2.3.44 cbf_column_name, cbf_set_column_name
PROTOTYPE
#include "cbf.h"
int cbf_column_name (cbf_handle handle, const char **columnname);
int cbf_set_column_name (cbf_handle handle, const char *newcolumnname)
DESCRIPTION
cbf_column_name sets *columnname to point to the name of the current
column of the current category.
The column name will be valid as long as the column exists.
The name must not be modified by the program in any way.
cbf_set_column_name sets the name of the current column to newcolumnname
ARGUMENTS
handle CBF handle.
columnname Pointer to the destination column name pointer.
newcolumnname New column name pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.31 cbf_find_column
----------------------------------------------------------------------
2.3.45 cbf_row_number
PROTOTYPE
#include "cbf.h"
int cbf_row_number (cbf_handle handle, unsigned int *row);
DESCRIPTION
cbf_row_number sets *row to the number of the current row of the current
category.
ARGUMENTS
handle CBF handle.
row Pointer to the destination row number.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.41 cbf_select_row
----------------------------------------------------------------------
2.3.46 cbf_get_value, cbf_require_value
PROTOTYPE
#include "cbf.h"
int cbf_get_value (cbf_handle handle, const char **value);
int cbf_require_value (cbf_handle handle, const char **value, const char
*defaultvalue );
DESCRIPTION
cbf_get_value sets *value to point to the ASCII value of the item at the
current column and row. cbf_require_value sets *value to point to the
ASCII value of the item at the current column and row, creating the data
item if necessary and initializing it to a copy of defaultvalue.
If the value is not ASCII, the function returns CBF_BINARY.
The value will be valid as long as the item exists and has not been set to
a new value.
The value must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
value Pointer to the destination value pointer.
defaultvalue Default value character string.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.47 cbf_set_value
PROTOTYPE
#include "cbf.h"
int cbf_set_value (cbf_handle handle, const char *value);
DESCRIPTION
cbf_set_value sets the item at the current column and row to the ASCII
value value.
ARGUMENTS
handle CBF handle.
value ASCII value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.48 cbf_get_typeofvalue
PROTOTYPE
#include "cbf.h"
int cbf_get_typeofvalue (cbf_handle handle, const char **typeofvalue);
DESCRIPTION
cbf_get_value sets *typeofvalue to point an ASCII descriptor of the value
of the item at the current column and row. The strings that may be
returned are:
"null" for a null value indicated by a "." or a "?"
"bnry" for a binary value
"word" for an unquoted string
"dblq" for a double-quoted string
"sglq" for a single-quoted string
"text" for a semicolon-quoted string (multiline text field)
"prns" for a parenthesis-bracketed string (multiline text field)
"brcs" for a brace-bracketed string (multiline text field)
"bkts" for a square-bracket-bracketed string (multiline text field)
"tsqs" for a treble-single-quote quoted string (multiline text field)
"tdqs" for a treble-double-quote quoted string (multiline text field)
Not all types are valid for all type of CIF files. In partcular the types
"prns", "brcs", "bkts" were introduced with DDLm and are not valid in DDL1
or DDL2 CIFS. The types "tsqs" and "tdqs" are not formally part of the CIF
syntax. A field for which no value has been set sets *typeofvalue to NULL
rather than to the string "null".
The typeofvalue must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
typeofvalue Pointer to the destination type-of-value string pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.49 cbf_set_typeofvalue
PROTOTYPE
#include "cbf.h"
int cbf_set_typeofvalue (cbf_handle handle, const char *typeofvalue);
DESCRIPTION
cbf_set_typeofvalue sets the type of the item at the current column and
row to the type specified by the ASCII character string given by
typeofvalue. The strings that may be used are:
"null" for a null value indicated by a "." or a "?"
"bnry" for a binary value
"word" for an unquoted string
"dblq" for a double-quoted string
"sglq" for a single-quoted string
"text" for a semicolon-quoted string (multiline text field)
"prns" for a parenthesis-bracketed string (multiline text field)
"brcs" for a brace-bracketed string (multiline text field)
"bkts" for a square-bracket-bracketed string (multiline text field)
"tsqs" for a treble-single-quote quoted string (multiline text field)
"tdqs" for a treble-double-quote quoted string (multiline text field)
Not all types may be used for all values. Not all types are valid for all
type of CIF files. In partcular the types "prns", "brcs", "bkts" were
introduced with DDLm and are not valid in DDL1 or DDL2 CIFS. The types
"tsqs" and "tdqs" are not formally part of the CIF syntax. No changes may
be made to the type of binary values. You may not set the type of a string
that contains a single quote followed by a blank or a tab or which
contains multiple lines to "sglq". You may not set the type of a string
that contains a double quote followed by a blank or a tab or which
contains multiple lines to "dblq".
ARGUMENTS
handle CBF handle.
typeofvalue ASCII string for desired type of value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.50 cbf_get_integervalue, cbf_require_integervalue
PROTOTYPE
#include "cbf.h"
int cbf_get_integervalue (cbf_handle handle, int *number);
int cbf_require_integervalue (cbf_handle handle, int *number, int
defaultvalue);
DESCRIPTION
cbf_get_integervalue sets *number to the value of the ASCII item at the
current column and row interpreted as a decimal integer.
cbf_require_integervalue sets *number to the value of the ASCII item at
the current column and row interpreted as a decimal integer, setting it to
defaultvalue if necessary.
If the value is not ASCII, the function returns CBF_BINARY.
ARGUMENTS
handle CBF handle.
number pointer to the number.
defaultvalue default number value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.51 cbf_set_integervalue
PROTOTYPE
#include "cbf.h"
int cbf_set_integervalue (cbf_handle handle, int number);
DESCRIPTION
cbf_set_integervalue sets the item at the current column and row to the
integer value number written as a decimal ASCII string.
ARGUMENTS
handle CBF handle.
number Integer value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
PROTOTYPE
#include "cbf.h"
int cbf_get_doublevalue (cbf_handle handle, double *number);
int cbf_require_doublevalue (cbf_handle handle, double *number, double
defaultvalue);
DESCRIPTION
cbf_get_doublevalue sets *number to the value of the ASCII item at the
current column and row interpreted as a decimal floating-point number.
cbf_require_doublevalue sets *number to the value of the ASCII item at the
current column and row interpreted as a decimal floating-point number,
setting it to defaultvalue if necessary.
If the value is not ASCII, the function returns CBF_BINARY.
ARGUMENTS
handle CBF handle.
number Pointer to the destination number.
defaultvalue default number value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.53 cbf_set_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.53 cbf_set_doublevalue
PROTOTYPE
#include "cbf.h"
int cbf_set_doublevalue (cbf_handle handle, const char *format, double
number);
DESCRIPTION
cbf_set_doublevalue sets the item at the current column and row to the
floating-point value number written as an ASCII string with the format
specified by format as appropriate for the printf function.
ARGUMENTS
handle CBF handle.
format Format for the number.
number Floating-point value.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims,
cbf_get_integerarrayparameters_wdims_fs,
cbf_get_integerarrayparameters_wdims_sf, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims,
cbf_get_realarrayparameters_wdims_fs, cbf_get_realarrayparameters_wdims_sf
PROTOTYPE
#include "cbf.h"
int cbf_get_integerarrayparameters (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement);
int cbf_get_integerarrayparameters_wdims (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement, const
char **byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_integerarrayparameters_wdims_fs (cbf_handle handle, unsigned
int *compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement, const
char **byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_integerarrayparameters_wdims_sf (cbf_handle handle, unsigned
int *compression, int *binary_id, size_t *elsize, int *elsigned, int
*elunsigned, size_t *elements, int *minelement, int *maxelement, const
char **byteorder, size_t *dimslow, size_t *dimmid, size_t *dimfast, size_t
*padding);
int cbf_get_realarrayparameters (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements);
int cbf_get_realarrayparameters_wdims (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements, const char
**byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_realarrayparameters_wdims_fs (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements, const char
**byteorder, size_t *dimfast, size_t *dimmid, size_t *dimslow, size_t
*padding);
int cbf_get_realarrayparameters_wdims_sf (cbf_handle handle, unsigned int
*compression, int *binary_id, size_t *elsize, size_t *elements, const char
**byteorder, size_t *dimslow, size_t *dimmid, size_t *dimfast, size_t
*padding);
DESCRIPTION
cbf_get_integerarrayparameters sets *compression, *binary_id, *elsize,
*elsigned, *elunsigned, *elements, *minelement and *maxelement to values
read from the binary value of the item at the current column and row. This
provides all the arguments needed for a subsequent call to
cbf_set_integerarray, if a copy of the array is to be made into another
CIF or CBF. cbf_get_realarrayparameters sets *compression, *binary_id,
*elsize, *elements to values read from the binary value of the item at the
current column and row. This provides all the arguments needed for a
subsequent call to cbf_set_realarray, if a copy of the arry is to be made
into another CIF or CBF.
The variants cbf_get_integerarrayparameters_wdims,
cbf_get_integerarrayparameters_wdims_fs,
cbf_get_integerarrayparameters_wdims_sf,
cbf_get_realarrayparameters_wdims, cbf_get_realarrayparameters_wdims_fs,
cbf_get_realarrayparameters_wdims_sf set **byteorder, *dimfast, *dimmid,
*dimslow, and *padding as well, providing the additional parameters needed
for a subsequent call to cbf_set_integerarray_wdims or
cbf_set_realarray_wdims.
The value returned in *byteorder is a pointer either to the string
"little_endian" or to the string "big_endian". This should be the byte
order of the data, not necessarily of the host machine. No attempt should
be made to modify this string. At this time only "little_endian" will be
returned.
The values returned in *dimfast, *dimmid and *dimslow are the sizes of the
fastest changing, second fastest changing and third fastest changing
dimensions of the array, if specified, or zero, if not specified.
The value returned in *padding is the size of the post-data padding, if
any and if specified in the data header. The value is given as a count of
octets.
If the value is not binary, the function returns CBF_ASCII.
ARGUMENTS
handle CBF handle.
compression Compression method used.
elsize Size in bytes of each array element.
binary_id Pointer to the destination integer binary identifier.
elsigned Pointer to an integer. Set to 1 if the elements can be
read as signed integers.
elunsigned Pointer to an integer. Set to 1 if the elements can be
read as unsigned integers.
elements Pointer to the destination number of elements.
minelement Pointer to the destination smallest element.
maxelement Pointer to the destination largest element.
byteorder Pointer to the destination byte order.
dimfast Pointer to the destination fastest dimension.
dimmid Pointer to the destination second fastest dimension.
dimslow Pointer to the destination third fastest dimension.
padding Pointer to the destination padding size.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.55 cbf_get_integerarray, cbf_get_realarray
PROTOTYPE
#include "cbf.h"
int cbf_get_integerarray (cbf_handle handle, int *binary_id, void *array,
size_t elsize, int elsigned, size_t elements, size_t *elements_read);
int cbf_get_realarray (cbf_handle handle, int *binary_id, void *array,
size_t elsize, size_t elements, size_t *elements_read);
DESCRIPTION
cbf_get_integerarray reads the binary value of the item at the current
column and row into an integer array. The array consists of elements
elements of elsize bytes each, starting at array. The elements are signed
if elsigned is non-0 and unsigned otherwise. *binary_id is set to the
binary section identifier and *elements_read to the number of elements
actually read. cbf_get_realarray reads the binary value of the item at the
current column and row into a real array. The array consists of elements
elements of elsize bytes each, starting at array. *binary_id is set to the
binary section identifier and *elements_read to the number of elements
actually read.
If any element in the integer binary data cant fit into the destination
element, the destination is set the nearest possible value.
If the value is not binary, the function returns CBF_ASCII.
If the requested number of elements cant be read, the function will read
as many as it can and then return CBF_ENDOFDATA.
Currently, the destination array must consist of chars, shorts or ints
(signed or unsigned). If elsize is not equal to sizeof (char), sizeof
(short) or sizeof (int), for cbf_get_integerarray, or sizeof(double) or
sizeof(float), for cbf_get_realarray the function returns CBF_ARGUMENT.
An additional restriction in the current version of CBFlib is that values
too large to fit in an int are not correctly decompressed. As an example,
if the machine with 32-bit ints is reading an array containing a value
outside the range 0 .. 2^32-1 (unsigned) or -2^31 .. 2^31-1 (signed), the
array will not be correctly decompressed. This restriction will be removed
in a future release. For cbf_get_realarray, only IEEE format is supported.
No conversion to other floating point formats is done at this time.
ARGUMENTS
handle CBF handle.
binary_id Pointer to the destination integer binary identifier.
array Pointer to the destination array.
elsize Size in bytes of each destination array element.
elsigned Set to non-0 if the destination array elements are
signed.
elements The number of elements to read.
elements_read Pointer to the destination number of elements actually
read.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.50 cbf_get_integervalue, cbf_require_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.56 cbf_set_integerarray,
cbf_set_integerarray_wdims, cbf_set_integerarray_wdims_fs,
cbf_set_integerarray_wdims_sf,
cbf_set_realarray,
cbf_set_realarray_wdims, cbf_set_realarray_wdims_fs,
cbf_set_realarray_wdims_sf
PROTOTYPE
#include "cbf.h"
int cbf_set_integerarray (cbf_handle handle, unsigned int compression, int
binary_id, void *array, size_t elsize, int elsigned, size_t elements);
int cbf_set_integerarray_wdims (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder, size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_integerarray_wdims_fs (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder, size_t dimfast, size_t dimmid,
size_t dimslow, size_t padding);
int cbf_set_integerarray_wdims_sf (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, int elsigned,
size_t elements, const char *byteorder, size_t dimslow, size_t dimmid,
size_t dimfast, size_t padding);
int cbf_set_realarray (cbf_handle handle, unsigned int compression, int
binary_id, void *array, size_t elsize, size_t elements);
int cbf_set_realarray_wdims (cbf_handle handle, unsigned int compression,
int binary_id, void *array, size_t elsize, size_t elements, const char
*byteorder, size_t dimfast, size_t dimmid, size_t dimslow, size_t
padding);
int cbf_set_realarray_wdims_fs (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, size_t elements,
const char *byteorder, size_t dimfast, size_t dimmid, size_t dimslow,
size_t padding);
int cbf_set_realarray_wdims_sf (cbf_handle handle, unsigned int
compression, int binary_id, void *array, size_t elsize, size_t elements,
const char *byteorder, size_t dimslow, size_t dimmid, size_t dimfast,
size_t padding);
DESCRIPTION
cbf_set_integerarray sets the binary value of the item at the current
column and row to an integer array. The array consists of elements
elements of elsize bytes each, starting at array. The elements are signed
if elsigned is non-0 and unsigned otherwise. binary_id is the binary
section identifier. cbf_set_realarray sets the binary value of the item at
the current column and row to an integer array. The array consists of
elements elements of elsize bytes each, starting at array. binary_id is
the binary section identifier.
The cbf_set_integerarray_wdims, cbf_set_integerarray_wdims_fs,
cbf_set_integerarray_wdims_sf, cbf_set_realarray_wdims,
cbf_set_realarray_wdims_fs and cbf_set_realarray_wdims_sf variants allow
the data header values of byteorder, dimfast, dimmid, dimslow and padding
to be set to the data byte order, the fastest, second fastest and third
fastest array dimensions and the size in byte of the post data padding to
be used.
The array will be compressed using the compression scheme specifed by
compression. Currently, the available schemes are:
CBF_CANONICAL Canonical-code compression (section 3.3.1)
CBF_PACKED CCP4-style packing (section 3.3.2)
CBF_PACKED_V2 CCP4-style packing, version 2 (section 3.3.2)
CBF_BYTE_OFFSET Simple "byte_offset" compression.
CBF_NONE No compression. NOTE: This scheme is by far the
slowest of the four and uses much more disk space. It is
intended for routine use with small arrays only. With
large arrays (like images) it should be used only for
debugging.
The values compressed are limited to 64 bits. If any element in the array
is larger than 64 bits, the value compressed is the nearest 64-bit value.
Currently, the source array must consist of chars, shorts or ints (signed
or unsigned), for cbf_set_integerarray, or IEEE doubles or floats for
cbf_set_realarray. If elsize is not equal to sizeof (char), sizeof (short)
or sizeof (int), the function returns CBF_ARGUMENT.
ARGUMENTS
handle CBF handle.
compression Compression method to use.
binary_id Integer binary identifier.
array Pointer to the source array.
elsize Size in bytes of each source array element.
elsigned Set to non-0 if the source array elements are signed.
elements: The number of elements in the array.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.53 cbf_set_doublevalue
2.3.54 cbf_get_integerarrayparameters,
cbf_get_integerarrayparameters_wdims, cbf_get_realarrayparameters,
cbf_get_realarrayparameters_wdims
2.3.55 cbf_get_integerarray, cbf_get_realarray
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.57 cbf_failnez
DEFINITION
#include "cbf.h"
#define cbf_failnez(f) {int err; err = (f); if (err) return err; }
DESCRIPTION
cbf_failnez is a macro used for error propagation throughout CBFlib.
cbf_failnez executes the function f and saves the returned error value. If
the error value is non-0, cbf_failnez executes a return with the error
value as argument. If CBFDEBUG is defined, then a report of the error is
also printed to the standard error stream, stderr, in the form
CBFlib error f in "symbol"
where f is the decimal value of the error and symbol is the symbolic form.
ARGUMENTS
f Integer error value.
SEE ALSO
2.3.58 cbf_onfailnez
----------------------------------------------------------------------
2.3.58 cbf_onfailnez
DEFINITION
#include "cbf.h"
#define cbf_onfailnez(f,c) {int err; err = (f); if (err) {{c; }return err;
}}
DESCRIPTION
cbf_onfailnez is a macro used for error propagation throughout CBFlib.
cbf_onfailnez executes the function f and saves the returned error value.
If the error value is non-0, cbf_failnez executes first the statement c
and then a return with the error value as argument. If CBFDEBUG is
defined, then a report of the error is also printed to the standard error
stream, stderr, in the form
CBFlib error f in "symbol"
where f is the decimal value of the error and symbol is the symbolic form.
ARGUMENTS
f integer function to execute.
c statement to execute on failure.
SEE ALSO
* 2.3.57 cbf_failnez
----------------------------------------------------------------------
2.3.59 cbf_require_datablock
PROTOTYPE
#include "cbf.h"
int cbf_require_datablock (cbf_handle handle, const char
*datablockname);
DESCRIPTION
cbf_require_datablock makes the data block with name datablockname the
current data block, if it exists, or creates it if it does not.
The comparison is case-insensitive.
The current category becomes undefined.
ARGUMENTS
handle CBF handle.
datablockname The name of the data block to find or create.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.21 cbf_rewind_datablock
2.3.25 cbf_next_datablock
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.42 cbf_datablock_name
2.3.60 cbf_require_category
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.60 cbf_require_category
PROTOTYPE
#include "cbf.h"
int cbf_require_category (cbf_handle handle, const char *categoryname);
DESCRIPTION
cbf_rewuire_category makes the category in the current data block with
name categoryname the current category, if it exists, or creates the
catagory if it does not exist.
The comparison is case-insensitive.
The current column and row become undefined.
ARGUMENTS
handle CBF handle.
categoryname The name of the category to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem
2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem
2.3.29 cbf_find_datablock
2.3.31 cbf_find_column
2.3.32 cbf_find_row
2.3.43 cbf_category_name
2.3.59 cbf_require_datablock
2.3.61 cbf_require_column
----------------------------------------------------------------------
2.3.61 cbf_require_column
PROTOTYPE
#include "cbf.h"
int cbf_require_column (cbf_handle handle, const char *columnname);
DESCRIPTION
cbf_require_column makes the columns in the current category with name
columnname the current column, if it exists, or creates it if it does
not.
The comparison is case-insensitive.
The current row is not affected.
ARGUMENTS
handle CBF handle.
columnname The name of column to find.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.19 cbf_rewind_column
2.3.27 cbf_next_column
2.3.29 cbf_find_datablock
2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem
2.3.32 cbf_find_row
2.3.44 cbf_column_name, cbf_set_column_name
2.3.59 cbf_require_datablock
2.3.60 cbf_require_category
----------------------------------------------------------------------
2.3.62 cbf_require_column_value
PROTOTYPE
#include "cbf.h"
int cbf_require_column_value (cbf_handle handle, const char *columnname,
const char **value, const char *defaultvalue);
DESCRIPTION
cbf_require_column_doublevalue sets *value to the ASCII item at the
current row for the column given with the name given by *columnname, or
to the string given by defaultvalue if the item cannot be found.
ARGUMENTS
handle CBF handle.
columnname Name of the column containing the number.
value pointer to the location to receive the value.
defaultvalue Value to use if the requested column and value cannot
be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.63 cbf_require_column_integervalue
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.63 cbf_require_column_integervalue
PROTOTYPE
#include "cbf.h"
int cbf_require_column_integervalue (cbf_handle handle, const char
*columnname, int *number, const int defaultvalue);
DESCRIPTION
cbf_require_column_doublevalue sets *number to the value of the ASCII
item at the current row for the column given with the name given by
*columnname, with the value interpreted as an integer number, or to the
number given by defaultvalue if the item cannot be found.
ARGUMENTS
handle CBF handle.
columnname Name of the column containing the number.
number pointer to the location to receive the integer value.
defaultvalue Value to use if the requested column and value cannot
be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.64 cbf_require_column_doublevalue
----------------------------------------------------------------------
2.3.64 cbf_require_column_doublevalue
PROTOTYPE
#include "cbf.h"
int cbf_require_column_doublevalue (cbf_handle handle, const char
*columnname, double *number, const double defaultvalue);
DESCRIPTION
cbf_require_column_doublevalue sets *number to the value of the ASCII
item at the current row for the column given with the name given by
*columnname, with the value interpreted as a decimal floating-point
number, or to the number given by defaultvalue if the item cannot be
found.
ARGUMENTS
handle CBF handle.
columnname Name of the column containing the number.
number pointer to the location to receive the floating-point
value.
defaultvalue Value to use if the requested column and value cannot
be found.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.3.46 cbf_get_value, cbf_require_value
2.3.47 cbf_set_value
2.3.48 cbf_get_typeofvalue
2.3.49 cbf_set_typeofvalue
2.3.51 cbf_set_integervalue
2.3.52 cbf_get_doublevalue, cbf_require_doublevalue
2.3.56 cbf_set_integerarray, cbf_set_integerarray_wdims,
cbf_set_realarray, cbf_set_realarray_wdims
2.3.62 cbf_require_column_value
2.3.63 cbf_require_column_integervalue
----------------------------------------------------------------------
2.3.65 cbf_get_local_integer_byte_order, cbf_get_local_real_byte_order,
cbf_get_local_real_format
PROTOTYPE
#include "cbf.h"
int cbf_get_local_integer_byte_order (char ** byte_order);
int cbf_get_local_real_byte_order (char ** byte_order);
int cbf_get_local_real_format (char ** real_format );
DESCRIPTION
cbf_get_local_integer_byte_order returns the byte order of integers on
the machine on which the API is being run in the form of a character
string returned as the value pointed to by byte_order.
cbf_get_local_real_byte_order returns the byte order of reals on the
machine on which the API is being run in the form of a character string
returned as the value pointed to by byte_order.
cbf_get_local_real_format returns the format of floats on the machine on
which the API is being run in the form of a character string returned as
the value pointed to by real_format. The strings returned must not be
modified in any way.
The values returned in byte_order may be the strings "little_endian" or
"big-endian". The values returned in real_format may be the strings
"ieee 754-1985" or "other". Additional values may be returned by future
versions of the API.
ARGUMENTS
byte_order pointer to the returned string
real_format pointer to the returned string
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.66 cbf_get_dictionary, cbf_set_dictionary, cbf_require_dictionary
PROTOTYPE
#include "cbf.h"
int cbf_get_dictionary (cbf_handle handle, cbf_handle * dictionary);
int cbf_set_dictionary (cbf_handle handle, cbf_handle dictionary_in);
int cbf_require_dictionary (cbf_handle handle, cbf_handle * dictionary)
DESCRIPTION
cbf_get_dictionary sets *dictionary to the handle of a CBF which has
been associated with the CBF handle by cbf_set_dictionary.
cbf_set_dictionary associates the CBF handle dictionary_in with handle
as its dictionary. cbf_require_dictionary sets *dictionary to the handle
of a CBF which has been associated with the CBF handle by
cbf_set_dictionary or creates a new empty CBF and associates it with
handle, returning the new handle in *dictionary.
ARGUMENTS
handle CBF handle.
dictionary Pointer to CBF handle of dictionary.
dictionary_in CBF handle of dcitionary.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.67 cbf_convert_dictionary
PROTOTYPE
#include "cbf.h"
int cbf_convert_dictionary (cbf_handle handle, cbf_handle dictionary )
DESCRIPTION
cbf_convert_dictionary converts dictionary as a DDL1 or DDL2 dictionary
to a CBF dictionary of category and item properties for handle, creating
a new dictionary if none exists or layering the definitions in
dictionary onto the existing dictionary of handle if one exists.
If a CBF is read into handle after calling cbf_convert_dictionary, then
the dictionary will be used for validation of the CBF as it is read.
ARGUMENTS
handle CBF handle.
dictionary CBF handle of dictionary.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.68 cbf_find_tag, cbf_find_local_tag
PROTOTYPE
#include "cbf.h"
int cbf_find_tag (cbf_handle handle, const char *tag)
int cbf_find_local_tag (cbf_handle handle, const char *tag)
DESCRIPTION
cbf_find_tag searches all of the CBF handle for the CIF tag given by the
string tag and makes it the current tag. The search does not include the
dictionary, but does include save frames as well as categories.
The string tag is the complete tag in either DDL1 or DDL2 format,
starting with the leading underscore, not just a category or column.
ARGUMENTS
handle CBF handle.
tag CIF tag.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.69 cbf_find_category_root, cbf_set_category_root,
cbf_require_category_root
PROTOTYPE
#include "cbf.h"
int cbf_find_category_root (cbf_handle handle, const char* categoryname,
const char** categoryroot);
int cbf_set_category_root (cbf_handle handle, const char*
categoryname_in, const char*categoryroot);
int cbf_require_category_root (cbf_handle handle, const char*
categoryname, const char** categoryroot);
DESCRIPTION
cbf_find_category_root sets *categoryroot to the root category of which
categoryname is an alias. cbf_set_category_root sets categoryname_in as
an alias of categoryroot in the dictionary associated with handle,
creating the dictionary if necessary. cbf_require_category_root sets
*categoryroot to the root category of which categoryname is an alias, if
there is one, or to the value of categoryname, if categoryname is not an
alias.
A returned categoryroot string must not be modified in any way.
ARGUMENTS
handle CBF handle.
categoryname category name which may be an alias.
categoryroot pointer to a returned category root name.
categoryroot_in input category root name.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.70 cbf_find_tag_root, cbf_set_tag_root, cbf_require_tag_root
PROTOTYPE
#include "cbf.h"
int cbf_find_tag_root (cbf_handle handle, const char* tagname, const
char** tagroot);
int cbf_set_tag_root (cbf_handle handle, const char* tagname, const
char*tagroot_in);
int cbf_require_tag_root (cbf_handle handle, const char* tagname, const
char** tagroot);
DESCRIPTION
cbf_find_tag_root sets *tagroot to the root tag of which tagname is an
alias. cbf_set_tag_root sets tagname as an alias of tagroot_in in the
dictionary associated with handle, creating the dictionary if necessary.
cbf_require_tag_root sets *tagroot to the root tag of which tagname is
an alias, if there is one, or to the value of tagname, if tagname is not
an alias.
A returned tagroot string must not be modified in any way.
ARGUMENTS
handle CBF handle.
tagname tag name which may be an alias.
tagroot pointer to a returned tag root name.
tagroot_in input tag root name.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.3.71 cbf_find_tag_category, cbf_set_tag_category
PROTOTYPE
#include "cbf.h"
int cbf_find_tag_category (cbf_handle handle, const char* tagname, const
char** categoryname);
int cbf_set_tag_category (cbf_handle handle, const char* tagname, const
char* categoryname_in);
DESCRIPTION
cbf_find_tag_category sets categoryname to the category associated with
tagname in the dictionary associated with handle. cbf_set_tag_category
upddates the dictionary associated with handle to indicated that tagname
is in category categoryname_in.
ARGUMENTS
handle CBF handle.
tagname tag name.
categoryname pointer to a returned category name.
categoryname_in input category name.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
----------------------------------------------------------------------
2.4 High-level function prototypes
2.4.1 cbf_read_template
PROTOTYPE
#include "cbf_simple.h"
int cbf_read_template (cbf_handle handle, FILE *file);
DESCRIPTION
cbf_read_template reads the CBF or CIF file file into the CBF object
specified by handle and selects the first datablock as the current
datablock.
ARGUMENTS
handle Pointer to a CBF handle.
file Pointer to a file descriptor.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.2 cbf_get_diffrn_id, cbf_require_diffrn_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_diffrn_id (cbf_handle handle, const char **diffrn_id);
int cbf_require_diffrn_id (cbf_handle handle, const char **diffrn_id,
const char *default_id)
DESCRIPTION
cbf_get_diffrn_id sets *diffrn_id to point to the ASCII value of the
"diffrn.id" entry. cbf_require_diffrn_id also sets *diffrn_id to point
to the ASCII value of the "diffrn.id" entry, but, if the "diffrn.id"
entry does not exist, it sets the value in the CBF and in*diffrn_id to
the character string given by default_id, creating the category and
column is necessary.
The diffrn_id will be valid as long as the item exists and has not been
set to a new value.
The diffrn_id must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
diffrn_id Pointer to the destination value pointer.
default_id Character string default value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.3 cbf_set_diffrn_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_diffrn_id (cbf_handle handle, const char *diffrn_id);
DESCRIPTION
cbf_set_diffrn_id sets the "diffrn.id" entry of the current datablock to
the ASCII value diffrn_id.
This function also changes corresponding "diffrn_id" entries in the
"diffrn_source", "diffrn_radiation", "diffrn_detector" and
"diffrn_measurement" categories.
ARGUMENTS
handle CBF handle.
diffrn_id ASCII value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.4 cbf_get_crystal_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_crystal_id (cbf_handle handle, const char **crystal_id);
DESCRIPTION
cbf_get_crystal_id sets *crystal_id to point to the ASCII value of the
"diffrn.crystal_id" entry.
If the value is not ASCII, the function returns CBF_BINARY.
The value will be valid as long as the item exists and has not been set
to a new value.
The value must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
crystal_id Pointer to the destination value pointer.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.5 cbf_set_crystal_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_crystal_id (cbf_handle handle, const char *crystal_id);
DESCRIPTION
cbf_set_crystal_id sets the "diffrn.crystal_id" entry to the ASCII value
crystal_id.
ARGUMENTS
handle CBF handle.
crystal_id ASCII value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.6 cbf_get_wavelength
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_wavelength (cbf_handle handle, double *wavelength);
DESCRIPTION
cbf_get_wavelength sets *wavelength to the current wavelength in AA.
ARGUMENTS
handle CBF handle.
wavelength Pointer to the destination.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.7 cbf_set_wavelength
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_wavelength (cbf_handle handle, double wavelength);
DESCRIPTION
cbf_set_wavelength sets the current wavelength in AA to wavelength.
ARGUMENTS
handle CBF handle.
wavelength Wavelength in AA.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.8 cbf_get_polarization
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_polarization (cbf_handle handle, double
*polarizn_source_ratio, double *polarizn_source_norm);
DESCRIPTION
cbf_get_polarization sets *polarizn_source_ratio and
*polarizn_source_norm to the corresponding source polarization
parameters.
Either destination pointer may be NULL.
ARGUMENTS
handle CBF handle.
polarizn_source_ratio Pointer to the destination
polarizn_source_ratio.
polarizn_source_norm Pointer to the destination
polarizn_source_norm.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.9 cbf_set_polarization
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_polarization (cbf_handle handle, double
polarizn_source_ratio, double polarizn_source_norm);
DESCRIPTION
cbf_set_polarization sets the source polarization to the values
specified by polarizn_source_ratio and polarizn_source_norm.
ARGUMENTS
handle CBF handle.
polarizn_source_ratio New value of polarizn_source_ratio.
polarizn_source_norm New value of polarizn_source_norm.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.10 cbf_get_divergence
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_divergence (cbf_handle handle, double *div_x_source, double
*div_y_source, double *div_x_y_source);
DESCRIPTION
cbf_get_divergence sets *div_x_source, *div_y_source and *div_x_y_source
to the corresponding source divergence parameters.
Any of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
div_x_source Pointer to the destination div_x_source.
div_y_source Pointer to the destination div_y_source.
div_x_y_source Pointer to the destination div_x_y_source.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.11 cbf_ set_divergence
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_divergence (cbf_handle handle, double div_x_source, double
div_y_source, double div_x_y_source);
DESCRIPTION
cbf_set_divergence sets the source divergence parameters to the values
specified by div_x_source, div_y_source and div_x_y_source.
ARGUMENTS
handle CBF handle.
div_x_source New value of div_x_source.
div_y_source New value of div_y_source.
div_x_y_source New value of div_x_y_source.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.12 cbf_count_elements
PROTOTYPE
#include "cbf_simple.h"
int cbf_count_elements (cbf_handle handle, unsigned int *elements);
DESCRIPTION
cbf_count_elements sets *elements to the number of detector elements.
ARGUMENTS
handle CBF handle.
elements Pointer to the destination count.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.13 cbf_get_element_id
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_element_id (cbf_handle handle, unsigned int element_number,
const char **element_id);
DESCRIPTION
cbf_get_element_id sets *element_id to point to the ASCII value of the
element_number'th "diffrn_data_frame.detector_element_id" entry,
counting from 0.
If the detector element does not exist, the function returns
CBF_NOTFOUND.
The element_id will be valid as long as the item exists and has not been
set to a new value.
The element_id must not be modified by the program in any way.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
element_id Pointer to the destination.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.14 cbf_get_gain
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_gain (cbf_handle handle, unsigned int element_number, double
*gain, double *gain_esd);
DESCRIPTION
cbf_get_gain sets *gain and *gain_esd to the corresponding gain
parameters for element number element_number.
Either of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
gain Pointer to the destination gain.
gain_esd Pointer to the destination gain_esd.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.15 cbf_ set_gain
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_gain (cbf_handle handle, unsigned int element_number, double
gain, double gain_esd);
DESCRIPTION
cbf_set_gain sets the gain of element number element_number to the
values specified by gain and gain_esd.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
gain New gain value.
gain_esd New gain_esd value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.16 cbf_get_overload
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_overload (cbf_handle handle, unsigned int element_number,
double *overload);
DESCRIPTION
cbf_get_overload sets *overload to the overload value for element number
element_number.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
overload Pointer to the destination overload.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.17 cbf_ set_overload
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_overload (cbf_handle handle, unsigned int element_number,
double overload);
DESCRIPTION
cbf_set_overload sets the overload value of element number
element_number to overload.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
overload New overload value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.18 cbf_get_integration_time
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_integration_time (cbf_handle handle, unsigned int reserved,
double *time);
DESCRIPTION
cbf_get_integration_time sets *time to the integration time in seconds.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Pointer to the destination time.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.19 cbf_set_integration_time
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_integration_time (cbf_handle handle, unsigned int reserved,
double time);
DESCRIPTION
cbf_set_integration_time sets the integration time in seconds to the
value specified by time. The parameter reserved is presently unused and
should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Integration time in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.20 cbf_get_timestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_timestamp (cbf_handle handle, unsigned int reserved, double
*time, int *timezone);
DESCRIPTION
cbf_get_timestamp sets *time to the collection timestamp in seconds
since January 1 1970. *timezone is set to timezone difference from UTC
in minutes. The parameter reserved is presently unused and should be set
to 0.
Either of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Pointer to the destination collection timestamp.
timezone Pointer to the destination timezone difference.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.21 cbf_set_timestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_timestamp (cbf_handle handle, unsigned int reserved, double
time, int timezone, double precision);
DESCRIPTION
cbf_set_timestamp sets the collection timestamp in seconds since January
1 1970 to the value specified by time. The timezone difference from UTC
in minutes is set to timezone. If no timezone is desired, timezone
should be CBF_NOTIM EZONE. The parameter reserved is presently unused
and should be set to 0.
The precision of the new timestamp is specified by the value precision
in seconds. If precision is 0, the saved timestamp is assumed accurate
to 1 second.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Timestamp in seconds since January 1 1970.
timezone Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
precision Timestamp precision in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.22 cbf_get_datestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_datestamp (cbf_handle handle, unsigned int reserved, int
*year, int *month, int *day, int *hour, int *minute, double *second, int
*timezone);
DESCRIPTION
cbf_get_datestamp sets *year, *month, *day, *hour, *minute and *second
to the corresponding values of the collection timestamp. *timezone is
set to timezone difference from UTC in minutes. The parameter <
i>reserved is presently unused and should be set to 0.
Any of the destination pointers may be NULL.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
year Pointer to the destination timestamp year.
month Pointer to the destination timestamp month (1-12).
day Pointer to the destination timestamp day (1-31).
hour Pointer to the destination timestamp hour (0-23).
minute Pointer to the destination timestamp minute (0-59).
second Pointer to the destination timestamp second (0-60.0).
timezone Pointer to the destination timezone difference from UTC in
minutes.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.23 cbf_set_datestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_datestamp (cbf_handle handle, unsigned int reserved, int
year, int month, int day, int hour, int minute, double second, int
timezone, double precision);
DESCRIPTION
cbf_set_datestamp sets the collection timestamp in seconds since January
1 1970 to the value specified by time. The timezone difference from UTC
in minutes is set to timezone. If no timezone is desired, timezone
should be CBF_NOTIM EZONE. The parameter reserved is presently unused
and should be set to 0.
The precision of the new timestamp is specified by the value precision
in seconds. If precision is 0, the saved timestamp is assumed accurate
to 1 second.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
time Timestamp in seconds since January 1 1970.
timezone Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
precision Timestamp precision in seconds.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.24 cbf_set_current_timestamp
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_current_timestamp (cbf_handle handle, unsigned int reserved,
int timezone);
DESCRIPTION
cbf_set_current_timestamp sets the collection timestamp to the current
time. The timezone difference from UTC in minutes is set to timezone. If
no timezone is desired, timezone should be CBF_NOTIMEZONE. If no
timezone is used, the timest amp will be UTC. The parameter reserved is
presently unused and should be set to 0.
The new timestamp will have a precision of 1 second.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
timezone Timezone difference from UTC in minutes or CBF_NOTIMEZONE.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.25 cbf_get_image_size, cbf_get_image_size_fs, cbf_get_image_size_sf,
cbf_get_3d_image_size, cbf_get_3d_image_size_fs,
cbf_get_3d_image_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_image_size (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimfast);
int cbf_get_image_size_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimfast, size_t *ndimslow);
int cbf_get_image_size_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimfast);
int cbf_get_3d_image_size (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimmid, size_t
*ndimfast);
int cbf_get_3d_image_size_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimfast, size_t *ndimmid, size_t
*ndimslow);
int cbf_get_3d_image_size_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, size_t *ndimslow, size_t *ndimmid, size_t
*ndimfast);
DESCRIPTION
cbf_get_image_size, cbf_get_image_size_fs and cbf_get_image_size_sf set
*ndimslow and *ndimfast to the slow and fast dimensions of the image
array for element number element_number. If the array is 1-dimensional,
*ndimslow will be set to the array size and *ndimfast will be set to 1.
If the array is 3-dimensional an error code will be returned.
cbf_get_3d_image_size, cbf_get_3d_image_size_fs and
cbf_get_3d_image_size_sf set *ndimslow, *ndimmid and *ndimfast to the
slowest, next fastest and fastest dimensions, respectively, of the 3D
image array for element number element_number. If the array is
1-dimensional, *ndimslow will be set to the array size and *ndimmid and
*ndimfast will be set to 1. If the array is 2-dimensional *ndimslow and
*ndimmid will be set as for a call to cbf_get_image_size and *ndimfast
will be set to 1.
The _fs calls give the dimensions in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the dimensions in
slow-to-fast order
Note that the ordering of dimensions is specified by values of the tag
_array_structure_list.precedence with a precedence of 1 for the fastest
dimension, 2 for the next slower, etc., which is opposite to the
ordering of the dimension arguments for these functions, except for the
ones with the _fs suffix..
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
ndimslow Pointer to the destination slowest dimension.
ndimmid Pointer to the destination next faster dimension.
ndimfast Pointer to the destination fastest dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.26 cbf_get_image, cbf_get_image_fs, cbf_get_image_sf,
cbf_get_real_image, cbf_get_real_image_fs, cbf_get_real_image_sf,
cbf_get_3d_image, cbf_get_3d_image_fs, cbf_get_3d_image_sf,
cbf_get_real_3d_image, cbf_get_real_3d_image_fs,
cbf_get_real_3d_image_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimslow, size_t ndimfast);
int cbf_get_image_fs (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimfast, size_t ndimslow);
int cbf_get_image_sf (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimslow, size_t ndimfast);
int cbf_get_real_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimfast);
int cbf_get_real_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimfast, size_t ndimslow);
int cbf_get_real_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimfast);
int cbf_get_3d_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, void *array, size_t elsize, int elsign, size_t
ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_3d_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, int elsign,
size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_get_3d_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, int elsign,
size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_real_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_get_real_3d_image_fs (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_get_real_3d_image_sf (cbf_handle handle, unsigned int reserved,
unsigned int element_number, void *array, size_t elsize, size_t
ndimslow, size_t ndimmid, size_t ndimfast);
DESCRIPTION
cbf_get_image, cbf_get_image_fs and cbf_get_image_sf read the image
array for element number element_number into an array. The array
consists of ndimslow *ndimfast elements of elsize bytes each, starting
at array. The elements are signed if elsign is non-0 and unsigned
otherwise. cbf_get_real_image, cbf_get_real_image_fs and
cbf_get_real_image_sf read the image array of IEEE doubles or floats for
element number element_number into an array. A real array is always
signed. cbf_get_3d_image, cbf_get_3d_image_fs and cbf_get_3d_image_sf
read the 3D image array for element number element_number into an array.
The array consists of ndimslow *ndimmid *ndimfast elements of elsize
bytes each, starting at array. The elements are signed if elsign is
non-0 and unsigned otherwise. cbf_get_real_3d_image,
cbf_get_real_3d_image_fs, cbf_get_real_3d_image_sf reads the 3D image
array of IEEE doubles or floats for element number element_number into
an array. A real array is always signed.
The _fs calls give the dimensions in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the dimensions in
slow-to-fast order
The structure of the array as a 1-, 2- or 3-dimensional array should
agree with the structure of the array given in the ARRAY_STRUCTURE_LIST
category. If the array is 1-dimensional, ndimslow should be the array
size and ndimfast and, for the 3D calls, ndimmid, should be set to 1
both in the call and in the imgCIF data being processed. If the array is
2-dimensional and a 3D call is used, ndimslow and ndimmid should be the
array dimensions and ndimfast should be set to 1 both in the call and in
the imgCIF data being processed.
If any element in the binary data canOt fit into the destination
element, the destination is set the nearest possible value.
If the value is not binary, the function returns CBF_ASCII.
If the requested number of elements canOt be read, the function will
read as many as it can and then return CBF_ENDOFDATA.
Currently, the destination array must consist of chars, shorts or ints
(signed or unsigned) for cbf_get_image, or IEEE doubles or floats for
cbf_get_real_image. If elsize is not equal to sizeof (char), sizeof
(short), sizeof (int), sizeof(double) or sizeof(float), the function
returns CBF_ARGUMENT.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
array Pointer to the destination array.
elsize Size in bytes of each destination array element.
elsigned Set to non-0 if the destination array elements are
signed.
ndimslow Slowest array dimension.
ndimmid Next faster array dimension.
ndimfast Fastest array dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.27 cbf_set_image, cbf_set_image_fs, cbf_set_image_sf,
cbf_set_real_image, cbf_set_real_image_fs, cbf_set_real_image_sf,
cbf_set_3d_image, cbf_set_3d_image, cbf_set_3d_image,
cbf_set_real_3d_image, cbf_set_real_3d_image_fs,
cbf_set_real_3d_image_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimslow, size_t ndimfast);
int cbf_set_image_fs(cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimfast, size_t ndimslow);
int cbf_set_image_sf(cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimslow, size_t ndimfast);
int cbf_set_real_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimfast);
int cbf_set_real_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimfast, size_t ndimslow);
int cbf_set_real_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimfast);
int cbf_set_3d_image (cbf_handle handle, unsigned int reserved, unsigned
int element_number, unsigned int compression, void *array, size_t
elsize, int elsign, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_set_3d_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void *array,
size_t elsize, int elsign, size_t ndimfast, size_t ndimmid, size_t
ndimslow);
int cbf_set_3d_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void *array,
size_t elsize, int elsign, size_t ndimslow, size_t ndimmid, size_t
ndimfast);
int cbf_set_real_3d_image (cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimmid, size_t ndimfast);
int cbf_set_real_3d_image_fs(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimfast, size_t ndimmid, size_t ndimslow);
int cbf_set_real_3d_image_sf(cbf_handle handle, unsigned int reserved,
unsigned int element_number, unsigned int compression, void
*array,size_t elsize, size_t ndimslow, size_t ndimmid, size_t ndimfast);
DESCRIPTION
cbf_set_image, cbf_set_image_fs and cbf_set_image_sf write the image
array for element number element_number. The array consists of ndimfast
*ndimslow elements of elsize bytes each, starting at array. The elements
are signed if elsign is non-zero and unsigned otherwise.
cbf_set_real_image, cbf_set_real_image_fs and cbf_set_real_image_sf
write the image array for element number element_number. The array
consists of ndimfast *ndimslow IEEE double or float elements of elsize
bytes each, starting at array. cbf_set_3d_image, cbf_set_3d_image_fs and
cbf_set_3d_image_sf write the 3D image array for element number
element_number. The array consists of ndimfast *ndimmid *ndimslow
elements of elsize bytes each, starting at array. The elements are
signed if elsign is non-0 and unsigned otherwise. cbf_set_real_3d_image,
cbf_set_real_3d_image_fs and cbf_set_real_3d_image_sf writes the 3D
image array for element number element_number. The array consists of
ndimfast *ndimmid *ndimslow IEEE double or float elements of elsize
bytes each, starting at array.
The _fs calls give the dimensions in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the dimensions in
slow-to-fast order
If the array is 1-dimensional, ndimslow should be the array size and
ndimfast and, for the 3D calls, ndimmid, should be set to 1. If the
array is 2-dimensional and the 3D calls are used, ndimslow and ndimmid
should be used for the array dimensions and ndimfast should be set to 1.
The array will be compressed using the compression scheme specifed by
compression. Currently, the available schemes are:
CBF_CANONICAL Canonical-code compression (section 3.3.1)
CBF_PACKED CCP4-style packing (section 3.3.2)
CBF_PACKED_V2 CCP4-style packing, version 2 (section 3.3.2)
CBF_BYTE_OFFSET Simple "byte_offset" compression.
CBF_NONE No compression.
The values compressed are limited to 64 bits. If any element in the
array is larger than 64 bits, the value compressed is the nearest 64-bit
value.
Currently, the source array must consist of chars, shorts or ints
(signed or unsigned)for cbf_set_image, or IEEE doubles or floats for
cbf_set_real_image. If elsize is not equal to sizeof (short), sizeof
(int), sizeof(double) or sizeof(float), the function returns
CBF_ARGUMENT.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
compression Compression type.
array Pointer to the image array.
elsize Size in bytes of each image array element.
elsigned Set to non-0 if the image array elements are signed.
ndimslow Slowest array dimension.
ndimmid Second slowest array dimension.
ndimfast Fastest array dimension.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.28 cbf_get_axis_setting
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_axis_setting (cbf_handle handle, unsigned int reserved,
const char *axis_id, double *start, double *increment);
DESCRIPTION
cbf_get_axis_setting sets *start and *increment to the corresponding
values of the axis axis_id.
Either of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
axis_id Axis id.
start Pointer to the destination start value.
increment Pointer to the destination increment value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.29 cbf_set_axis_setting
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_axis_setting (cbf_handle handle, unsigned int reserved,
const char *axis_id, double start, double increment);
DESCRIPTION
cbf_set_axis_setting sets the starting and increment values of the axis
axis_id to start and increment.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
handle CBF handle.
reserved Unused. Any value other than 0 is invalid.
axis_id Axis id.
start Start value.
increment Increment value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.30 cbf_construct_goniometer
PROTOTYPE
#include "cbf_simple.h"
int cbf_construct_goniometer (cbf_handle handle, cbf_goniometer
*goniometer);
DESCRIPTION
cbf_construct_goniometer constructs a goniometer object using the
description in the CBF object handle and initialises the goniometer
handle *goniometer.
ARGUMENTS
handle CBF handle.
goniometer Pointer to the destination goniometer handle.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.31 cbf_free_goniometer
PROTOTYPE
#include "cbf_simple.h"
int cbf_free_goniometer (cbf_goniometer goniometer);
DESCRIPTION
cbf_free_goniometer destroys the goniometer object specified by
goniometer and frees all associated memory.
ARGUMENTS
goniometer Goniometer handle to free.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.32 cbf_get_rotation_axis
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_rotation_axis (cbf_goniometer goniometer, unsigned int
reserved, double *vector1, double *vector2, double *vector3);
DESCRIPTION
cbf_get_rotation_axis sets *vector1, *vector2, and *vector3 to the 3
components of the goniometer rotation axis used for the exposure.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
vector1 Pointer to the destination x component of the rotation
axis.
vector2 Pointer to the destination y component of the rotation
axis.
vector3 Pointer to the destination z component of the rotation
axis.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.33 cbf_get_rotation_range
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_rotation_range (cbf_goniometer goniometer, unsigned int
reserved, double *start, double *increment);
DESCRIPTION
cbf_get_rotation_range sets *start and *increment to the corresponding
values of the goniometer rotation axis used for the exposure.
Either of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
start Pointer to the destination start value.
increment Pointer to the destination increment value.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.34 cbf_rotate_vector
PROTOTYPE
#include "cbf_simple.h"
int cbf_rotate_vector (cbf_goniometer goniometer, unsigned int reserved,
double ratio, double initial1, double initial2, double initial3, double
*final1, double *final2, double *final3);
DESCRIPTION
cbf_rotate_vector sets *final1, *final2, and *final3 to the 3 components
of the of the vector (initial1, initial2, initial3) after reorientation
by applying the goniometer rotations. The value ratio specif ies the
goniometer setting and varies from 0.0 at the beginning of the exposure
to 1.0 at the end, irrespective of the actual rotation range.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
ratio Goniometer setting. 0 = beginning of exposure, 1 = end.
initial1 x component of the initial vector.
initial2 y component of the initial vector.
initial3 z component of the initial vector.
vector1 Pointer to the destination x component of the final
vector.
vector2 Pointer to the destination y component of the final
vector.
vector3 Pointer to the destination z component of the final
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.35 cbf_get_reciprocal
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_reciprocal (cbf_goniometer goniometer, unsigned int
reserved, double ratio, double wavelength, double real1, double real2,
double real3, double *reciprocal1, double *reciprocal2, double
*reciprocal3);
DESCRIPTION
cbf_get_reciprocal sets *reciprocal1, * reciprocal2, and * reciprocal3
to the 3 components of the of the reciprocal-space vector corresponding
to the real-space vector (real1, real2, real3). The reciprocal-space
vector is oriented to correspond to the goniometer setting with all axes
at 0. The value wavelength is the wavlength in AA and the value ratio
specifies the current goniometer setting and varies from 0.0 at the
beginning of the exposur e to 1.0 at the end, irrespective of the actual
rotation range.
Any of the destination pointers may be NULL.
The parameter reserved is presently unused and should be set to 0.
ARGUMENTS
goniometer Goniometer handle.
reserved Unused. Any value other than 0 is invalid.
ratio Goniometer setting. 0 = beginning of exposure, 1 = end.
wavelength Wavelength in AA.
real1 x component of the real-space vector.
real2 y component of the real-space vector.
real3 z component of the real-space vector.
reciprocal1 Pointer to the destination x component of the
reciprocal-space vector.
reciprocal2 Pointer to the destination y component of the
reciprocal-space vector.
reciprocal3 Pointer to the destination z component of the
reciprocal-space vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.36 cbf_construct_detector, cbf_construct_reference_detector,
cbf_require_reference_detector
PROTOTYPE
#include "cbf_simple.h"
int cbf_construct_detector (cbf_handle handle, cbf_detector *detector,
unsigned int element_number);
int cbf_construct_reference_detector (cbf_handle handle, cbf_detector
*detector, unsigned int element_number);
int cbf_require_reference_detector (cbf_handle handle, cbf_detector
*detector, unsigned int element_number);
DESCRIPTION
cbf_construct_detector constructs a detector object for detector element
number element_number using the description in the CBF object handle and
initialises the detector handle *detector.
cbf_construct_reference_detector constructs a detector object for
detector element number element_number using the description in the CBF
object handle and initialises the detector handle *detector using the
reference settings of the axes. cbf_require_reference_detector is
similar, but try to force the creations of missing intermediate
categories needed to construct a detector object.
ARGUMENTS
handle CBF handle.
detector Pointer to the destination detector handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.37 cbf_free_detector
PROTOTYPE
#include "cbf_simple.h"
int cbf_free_detector (cbf_detector detector);
DESCRIPTION
cbf_free_detector destroys the detector object specified by detector and
frees all associated memory.
ARGUMENTS
detector Detector handle to free.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.38 cbf_get_beam_center, cbf_get_beam_center_fs, cbf_get_beam_center_sf,
cbf_set_beam_center, cbf_set_beam_center_fs, cbf_set_beam_center_sf,
set_reference_beam_center, set_reference_beam_center_fs,
set_reference_beam_center_fs
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_beam_center (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_get_beam_center_fs (cbf_detector detector, double *indexfast,
double *indexslow, double *centerfast, double *centerslow);
int cbf_get_beam_center_sf (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_set_beam_center (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_set_beam_center_fs (cbf_detector detector, double *indexfast,
double *indexslow, double *centerfast, double *centerslow);
int cbf_set_beam_center_sf (cbf_detector detector, double *indexslow,
double *indexfast, double *centerslow, double *centerfast);
int cbf_set_reference_beam_center (cbf_detector detector, double
*indexslow, double *indexfast, double *centerslow, double *centerfast);
int cbf_set_reference_beam_center_fs (cbf_detector detector, double
*indexfast, double *indexslow, double *centerfast, double *centerslow);
int cbf_set_reference_beam_center_sf (cbf_detector detector, double
*indexslow, double *indexfast, double *centerslow, double *centerfast);
DESCRIPTION
cbf_get_beam_center sets *centerfast and *centerslow to the
displacements in mm along the detector axes from pixel (0, 0) to the
point at which the beam intersects the detector and *indexfast and
*indexslow to the corresponding indices. cbf_set_beam_center sets the
offsets in the axis category for the detector element axis with
precedence 1 to place the beam center at the position given in mm by
*centerfast and *centerslow as the displacements in mm along the
detector axes from pixel (0, 0) to the point at which the beam
intersects the detector at the indices given *indexfast and *indexslow.
cbf_set_reference_beam_center sets the displacments in the
array_structure_list_axis category to place the beam center at the
position given in mm by *centerfast and *centerslow as the displacements
in mm along the detector axes from pixel (0, 0) to the point at which
the beam intersects the detector at the indices given by *indexfast and
*indexslow. In order to achieve consistent results, a reference detector
should be used for detector to have all axes at their reference
settings.
Note that the precedence 1 axis is the fastest axis, so that *centerfast
and *indexfast are the fast axis components of the center and
*centerslow and *indexslow are the slow axis components of the center.
The _fs calls give the displacments in a fast-to-slow order. The calls
with no suffix and the calls _sf calls give the displacements in
slow-to-fast order
Any of the destination pointers may be NULL for getting the beam center.
For setting the beam axis, either the indices of the center must not be
NULL.
The indices are non-negative for beam centers within the detector
surface, but the center for an axis with a negative increment will be
negative for a beam center within the detector surface.
For cbf_set_beam_center if the diffrn_data_frame category exists with a
row for the corresponding element id, the values will be set for
_diffrn_data_frame.center_fast and _diffrn_data_frame.center_slow in
millimetres and the value of _diffrn_data_frame.center_units will be set
to 'mm'.
For cbf_set_reference_beam_center if the diffrn_detector_element
category exists with a row for the corresponding element id, the values
will be set for _diffrn_detector_element.reference_center_fast and
_diffrn_detector_element.reference_center_slow in millimetres and the
value of _diffrn_detector_element.reference_units will be set to 'mm'.
ARGUMENTS
detector Detector handle.
indexfast Pointer to the destination fast index.
indexslow Pointer to the destination slow index.
centerfast Pointer to the destination displacement along the fast
axis.
centerslow Pointer to the destination displacement along the slow
axis.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.39 cbf_get_detector_distance
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_detector_distance (cbf_detector detector, double *distance);
DESCRIPTION
cbf_get_detector_distance sets *distance to the nearest distance from
the sample position to the detector plane.
ARGUMENTS
detector Detector handle.
distance Pointer to the destination distance.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.40 cbf_get_detector_normal
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_detector_normal (cbf_detector detector, double *normal1,
double *normal2, double *normal3);
DESCRIPTION
cbf_get_detector_normal sets *normal1, *normal2, and *normal3 to the 3
components of the of the normal vector to the detector plane. The vector
is normalized.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
normal1 Pointer to the destination x component of the normal
vector.
normal2 Pointer to the destination y component of the normal
vector.
normal3 Pointer to the destination z component of the normal
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.41 cbf_get_detector_axis_slow, cbf_get_detector_axis_slow,
cbf_get_detector_axes, cbf_get_detector_axes_fs, cbf_get_detector_axes_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_detector_axis_slow (cbf_detector detector, double
*slowaxis1, double *slowaxis2, double *slowaxis3);
int cbf_get_detector_axis_fast (cbf_detector detector, double
*fastaxis1, double *fastaxis2, double *fastaxis3);
int cbf_get_detector_axes (cbf_detector detector, double *slowaxis1,
double *slowaxis2, double *slowaxis3, double *fastaxis1, double
*fastaxis2, double *fastaxis3);
int cbf_get_detector_axes_fs (cbf_detector detector, double *fastaxis1,
double *fastaxis2, double *fastaxis3, double *slowaxis1, double
*slowaxis2, double *slowaxis3);
int cbf_get_detector_axes_sf (cbf_detector detector, double *slowaxis1,
double *slowaxis2, double *slowaxis3, double *fastaxis1, double
*fastaxis2, double *fastaxis3);
DESCRIPTION
cbf_get_detector_axis_slow sets *slowaxis1, *slowaxis2, and *slowaxis3
to the 3 components of the slow axis of the specified detector at the
current settings of all axes. cbf_get_detector_axis_slow sets
*fastaxis1, *fastaxis2, and *fastaxis3 to the 3 components of the fast
axis of the specified detector at the current settings of all axes.
cbf_get_detector_axes, cbf_get_detector_axes_fs and int
cbf_get_detector_axes_sf set *slowaxis1, *slowaxis2, and *slowaxis3 to
the 3 components of the slow axis and *fastaxis1, *fastaxis2, and
*fastaxis3 to the 3 components of the fast axis of the specified
detector at the current settings of all axes.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
slowaxis1 Pointer to the destination x component of the slow axis
vector.
slowaxis2 Pointer to the destination y component of the slow axis
vector.
slowaxis3 Pointer to the destination z component of the slow axis
vector.
fastaxis1 Pointer to the destination x component of the fast axis
vector.
fastaxis2 Pointer to the destination y component of the fast axis
vector.
fastaxis3 Pointer to the destination z component of the fast axis
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.42 cbf_get_pixel_coordinates, cbf_get_pixel_coordinates_fs,
cbf_get_pixel_coordinates_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_coordinates (cbf_detector detector, double indexslow,
double indexfast, double *coordinate1, double *coordinate2, double
*coordinate3);
int cbf_get_pixel_coordinates_fs (cbf_detector detector, double
indexfast, double indexslow, double *coordinate1, double *coordinate2,
double *coordinate3);
int cbf_get_pixel_coordinates_sf (cbf_detector detector, double
indexslow, double indexfast, double *coordinate1, double *coordinate2,
double *coordinate3);
DESCRIPTION
cbf_get_pixel_coordinates, cbf_get_pixel_coordinates_fs and
cbf_get_pixel_coordinates_sf ses *coordinate1, *coordinate2, and
*coordinate3 to the vector position of pixel (indexfast, indexslow) on
the detector surface. If indexslow and indexfast are integers then the
coordinates correspond to the center of a pixel.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
indexslow Slow index.
indexfast Fast index.
coordinate1 Pointer to the destination x component.
coordinate2 Pointer to the destination y component.
coordinate3 Pointer to the destination z component.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.43 cbf_get_pixel_normal, cbf_get_pixel_normal_fs,
cbf_get_pixel_normal_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_normal (cbf_detector detector, double indexslow,
double indexfast, double *normal1, double *normal2, double *normal3);
int cbf_get_pixel_normal_fs (cbf_detector detector, double indexfast,
double indexslow, double *normal1, double *normal2, double *normal3);
int cbf_get_pixel_normal (cbf_detector detector, double indexslow,
double indexfast, double *normal1, double *normal2, double *normal3);
DESCRIPTION
cbf_get_detector_normal, cbf_get_pixel_normal_fs and
cbf_get_pixel_normal_sf set *normal1, *normal2, and *normal3 to the 3
components of the of the normal vector to the pixel at (indexfast,
indexslow). The vector is normalized.
Any of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
indexslow Slow index.
indexfast Fast index.
normal1 Pointer to the destination x component of the normal
vector.
normal2 Pointer to the destination y component of the normal
vector.
normal3 Pointer to the destination z component of the normal
vector.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.44 cbf_get_pixel_area, cbf_get_pixel_area_fs, cbf_get_pixel_area_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_area (cbf_detector detector, double indexslow, double
indexfast, double *area, double *projected_area);
int cbf_get_pixel_area_fs(cbf_detector detector, double indexfast,
double indexslow, double *area, double *projected_area);
int cbf_get_pixel_area_sf(cbf_detector detector, double indexslow,
double indexfast, double *area, double *projected_area);
DESCRIPTION
cbf_get_pixel_area, cbf_get_pixel_area_fs and cbf_get_pixel_area_sf set
*area to the area of the pixel at (indexfast, indexslow) on the detector
surface and *projected_area to the apparent area of the pixel as viewed
from the sample position, with indexslow being the slow axis and
indexfast being the fast axis.
Either of the destination pointers may be NULL.
ARGUMENTS
detector Detector handle.
indexfast Fast index.
indexslow Slow index.
area Pointer to the destination area in mm2.
projected_area Pointer to the destination apparent area in mm2.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.45 cbf_get_pixel_size, cbf_get_pixel_size_fs, cbf_get_pixel_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_pixel_size (cbf_handle handle, unsigned int element_number,
int axis_number, double *psize);
int cbf_get_pixel_size_fs(cbf_handle handle, unsigned int
element_number, int axis_number, double *psize);
int cbf_get_pixel_size_sf(cbf_handle handle, unsigned int
element_number, int axis_number, double *psize);
DESCRIPTION
cbf_get_pixel_size and cbf_get_pixel_size_sf set *psize to point to the
double value in millimeters of the axis axis_number of the detector
element element_number. The axis_number is numbered from 1, starting
with the slowest axis. cbf_get_pixel_size_fs sets *psize to point to the
double value in millimeters of the axis axis_number of the detector
element element_number. The axis_number is numbered from 1, starting
with the fastest axis.
If a negative axis number is given, the order of axes is reversed, so
that -1 specifies the slowest axis for cbf_get_pixel_size_fs and the
fastest axis for cbf_get_pixel_size_sf.
If the pixel size is not given explcitly in the "array_element_size"
category, the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
axis_number The number of the axis, starting from 1 for the
fastest for cbf_get_pixel_size and
cbf_get_pixel_size_fs and the slowest for
cbf_get_pixel_size_sf.
psize Pointer to the destination pixel size.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.46 cbf_set_pixel_size, cbf_set_pixel_size_fs, cbf_set_pixel_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_pixel_size (cbf_handle handle, unsigned int element_number,
int axis_number, double psize);
int cbf_set_pixel_size_fs(cbf_handle handle, unsigned int
element_number, int axis_number, double psize);
int cbf_set_pixel_size_sf(cbf_handle handle, unsigned int
element_number, int axis_number, double psize);
DESCRIPTION
cbf_set_pixel_size and cbf_set_pixel_size_sf set the item in the
"e;size"e; column of the "array_structure_list" category at the
row which matches axis axis_number of the detector element
element_number converting the double pixel size psize from meters to
millimeters in storing it in the "size" column for the axis axis_number
of the detector element element_number. The axis_number is numbered from
1, starting with the slowest axis. cbf_set_pixel_size_fs sets the item
in the "e;size"e; column of the "array_structure_list" category
at the row which matches axis axis_number of the detector element
element_number converting the double pixel size psize from meters to
millimeters in storing it in the "size" column for the axis axis_number
of the detector element element_number. The axis_number is numbered from
1, starting with the fastest axis.
If a negative axis number is given, the order of axes is reversed, so
that -1 specifies the slowest axis for cbf_get_pixel_size_fs and the
fastest axis for cbf_get_pixel_size_sf.
If the "array_structure_list" category does not already exist, it is
created.
If the appropriate row in the "array_structure_list" catgeory does not
already exist, it is created.
If the pixel size is not given explcitly in the "array_element_size
category", the function returns CBF_NOTFOUND.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
axis_number The number of the axis, fastest first, starting from
1.
psize The pixel size in millimeters.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.47 cbf_get_inferred_pixel_size, cbf_get_inferred_pixel_size_fs,
cbf_get_inferred_pixel_size_sf
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_inferred_pixel_size (cbf_detector detector, int axis_number,
double *psize);
int cbf_get_inferred_pixel_size_fs(cbf_detector detector, int
axis_number, double *psize);
int cbf_get_inferred_pixel_size_sf(cbf_detector detector, int
axis_number, double *psize);
DESCRIPTION
cbf_get_inferred_pixel_size, cbf_get_inferred_pixel_size_sf set *psize
to point to the double value in millimeters of the pixel size for the
axis axis_number value. The slow index is treated as axis 1 and the next
faster index is treated as axis 2. cbf_get_inferred_pixel_size_fs sets
*psize to point to the double value in millimeters of the pixel size for
the axis axis_number value. The fast index is treated as axis 1 and the
next slower index is treated as axis 2.
If the axis number is negative, the axes are used in the reverse order
so that an axis_number of -1 indicates the fast axes in a call to
cbf_get_inferred_pixel_size or cbf_get_inferred_pixel_size_sf and
indicates the fast axis in a call to cbf_get_inferred_pixel_size_fs.
ARGUMENTS
detector Detector handle.
axis_number The number of the axis.
area Pointer to the destination pizel size in mm.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.48 cbf_get_unit_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_unit_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_get_unit_cell sets cell[0:2] to the double values of the cell edge
lengths a, b and c in AAngstroms, cell[3:5] to the double values of the
cell angles a, b and g in degrees, cell_esd[0:2] to the double values of
the estimated strandard deviations of the cell edge lengths a, b and c
in AAngstroms, cell_esd[3:5] to the double values of the estimated
standard deviations of the the cell angles a, b and g in degrees.
The values returned are retrieved from the first row of the "cell"
category. The value of "_cell.entry_id" is ignored.
cell or cell_esd may be NULL.
If cell is NULL, the cell parameters are not retrieved.
If cell_esd is NULL, the cell parameter esds are not retrieved.
If the "cell" category is present, but some of the values are missing,
zeros are returned for the missing values.
ARGUMENTS
handle CBF handle.
cell Pointer to the destination array of 6 doubles for the cell
parameters.
cell_esd Pointer to the destination array of 6 doubles for the cell
parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success. No errors is returned
for missing values if the "cell" category exists.
SEE ALSO
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.49 cbf_set_unit_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_unit_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_set_unit_cell sets the cell parameters to the double values given in
cell[0:2] for the cell edge lengths a, b and c in AAngstroms, the double
values given in cell[3:5] for the cell angles a, b and g in degrees, the
double values given in cell_esd[0:2] for the estimated strandard
deviations of the cell edge lengths a, b and c in AAngstroms, and the
double values given in cell_esd[3:5] for the estimated standard
deviations of the the cell angles a, b and g in degrees.
The values are placed in the first row of the "cell" category. If no
value has been given for "_cell.entry_id", it is set to the value of the
"diffrn.id" entry of the current data block.
cell or cell_esd may be NULL.
If cell is NULL, the cell parameters are not set.
If cell_esd is NULL, the cell parameter esds are not set.
If the "cell" category is not present, it is created. If any of the
necessary columns are not present, they are created.
ARGUMENTS
handle CBF handle.
cell Pointer to the array of 6 doubles for the cell parameters.
cell_esd Pointer to the array of 6 doubles for the cell parameter
esds.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
SEE ALSO
2.4.50 cbf_get_reciprocal_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_reciprocal_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_get_reciprocal_cell sets cell[0:2] to the double values of the
reciprocal cell edge lengths a*, b* and c* in AAngstroms-1, cell[3:5] to
the double values of the reciprocal cell angles a*, b* and g* in
degrees, cell_esd[0:2] to the double values of the estimated strandard
deviations of the reciprocal cell edge lengths a*, b* and c* in
AAngstroms-1, cell_esd[3:5] to the double values of the estimated
standard deviations of the the reciprocal cell angles a*, b* and g* in
degrees.
The values returned are retrieved from the first row of the "cell"
category. The value of "_cell.entry_id" is ignored.
cell or cell_esd may be NULL.
If cell is NULL, the reciprocal cell parameters are not retrieved.
If cell_esd is NULL, the reciprocal cell parameter esds are not
retrieved.
If the "cell" category is present, but some of the values are missing,
zeros are returned for the missing values.
ARGUMENTS
handle CBF handle.
cell Pointer to the destination array of 6 doubles for the
reciprocal cell parameters.
cell_esd Pointer to the destination array of 6 doubles for the
reciprocal cell parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success. No errors is returned
for missing values if the "cell" category exists.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.51 cbf_set_reciprocal_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_set_reciprocal_cell (cbf_handle handle, double cell[6], double
cell_esd[6] );
DESCRIPTION
cbf_set_reciprocal_cell sets the reciprocal cell parameters to the
double values given in cell[0:2] for the reciprocal cell edge lengths
a*, b* and c* in AAngstroms-1, the double values given in cell[3:5] for
the reciprocal cell angles a*, b* and g* in degrees, the double values
given in cell_esd[0:2] for the estimated strandard deviations of the
reciprocal cell edge lengths a*, b* and c* in AAngstroms, and the double
values given in cell_esd[3:5] for the estimated standard deviations of
the reciprocal cell angles a*, b* and g* in degrees.
The values are placed in the first row of the "cell" category. If no
value has been given for "_cell.entry_id", it is set to the value of the
"diffrn.id" entry of the current data block.
cell or cell_esd may be NULL.
If cell is NULL, the reciprocal cell parameters are not set.
If cell_esd is NULL, the reciprocal cell parameter esds are not set.
If the "cell" category is not present, it is created. If any of the
necessary columns are not present, they are created.
ARGUMENTS
handle CBF handle.
cell Pointer to the array of 6 doubles for the reciprocal cell
parameters.
cell_esd Pointer to the array of 6 doubles for the reciprocal cell
parameter esds.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.52 cbf_compute_cell_volume
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.52 cbf_compute_cell_volume
PROTOTYPE
#include "cbf_simple.h"
int cbf_compute_cell_volume ( double cell[6], double *volume );
DESCRIPTION
cbf_compute_cell_volume sets *volume to point to the volume of the unit
cell computed from the double values in cell[0:2] for the cell edge
lengths a, b and c in AAngstroms and the double values given in
cell[3:5] for the cell angles a, b and g in degrees.
ARGUMENTS
cell Pointer to the array of 6 doubles giving the cell parameters.
volume Pointer to the doubles for cell volume.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.53 cbf_compute_reciprocal_cell
----------------------------------------------------------------------
2.4.53 cbf_compute_reciprocal_cell
PROTOTYPE
#include "cbf_simple.h"
int cbf_compute_reciprocal_cell ( double cell[6], double rcell[6] );
DESCRIPTION
cbf_compute_reciprocal_cell sets rcell to point to the array of
reciprocal cell parameters computed from the double values cell[0:2]
giving the cell edge lengths a, b and c in AAngstroms, and the double
values cell[3:5] giving the cell angles a, b and g in degrees. The
double values rcell[0:2] will be set to the reciprocal cell lengths a*,
b* and c* in AAngstroms-1 and the double values rcell[3:5] will be set
to the reciprocal cell angles a*, b* and g* in degrees.
ARGUMENTS
cell Pointer to the array of 6 doubles giving the cell parameters.
rcell Pointer to the destination array of 6 doubles giving the
reciprocal cell parameters.
volume Pointer to the doubles for cell volume.
RETURN VALUE
Returns an error code on failure or 0 for success.
SEE ALSO
2.4.48 cbf_get_unit_cell
2.4.49 cbf_set_unit_cell
2.4.50 cbf_get_reciprocal_cell
2.4.51 cbf_set_reciprocal_cell
2.4.52 cbf_compute_cell_volume
----------------------------------------------------------------------
2.4.54 cbf_get_orientation_matrix, cbf_set_orientation_matrix
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_orientation_matrix (cbf_handle handle, double ub_matrix[9]);
int cbf_set_orientation_matrix (cbf_handle handle, double ub_matrix[9]);
DESCRIPTION
cbf_get_orientation_matrix sets ub_matrix to point to the array of
orientation matrix entries in the "diffrn" category in the order of
columns:
"UB[1][1]" "UB[1][2]" "UB[1][3]"
"UB[2][1]" "UB[2][2]" "UB[2][3]"
"UB[3][1]" "UB[3][2]" "UB[3][3]"
cbf_set_orientation_matrix sets the values in the "diffrn" category to
the values pointed to by ub_matrix.
ARGUMENTS
handle CBF handle.
ubmatric Source or destination array of 9 doubles giving the
orientation matrix parameters.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.4.55 cbf_get_bin_sizes, cbf_set_bin_sizes
PROTOTYPE
#include "cbf_simple.h"
int cbf_get_bin_sizes(cbf_handle handle, unsigned int element_number,
double * slowbinsize, double * fastbinsize);
int cbf_set_bin_sizes(cbf_handle handle, unsigned int element_number,
double slowbinsize_in,double fastbinsize_in);
DESCRIPTION
cbf_get_bin_sizes sets slowbinsize to point to the value of the number
of pixels composing one array element in the dimension that changes at
the second-fastest rate and fastbinsize to point to the value of the
number of pixels composing one array element in the dimension that
changes at the fastest rate for the dectector element with the ordinal
element_number. cbf_set_bin_sizes sets the the pixel bin sizes in the
"array_intensities" category to the values of slowbinsize_in for the
number of pixels composing one array element in the dimension that
changes at the second-fastest rate and fastbinsize_in for the number of
pixels composing one array element in the dimension that changes at the
fastest rate for the dectector element with the ordinal element_number.
In order to allow for software binning involving fractions of pixels,
the bin sizes are doubles rather than ints.
ARGUMENTS
handle CBF handle.
element_number The number of the detector element counting from 0 by
order of appearance in the "diffrn_data_frame"
category.
slowbinsize Pointer to the returned number of pixels composing
one array element in the dimension that changes at the
second-fastest rate.
fastbinsize Pointer to the returned number of pixels composing
one array element in the dimension that changes at the
fastest rate.
slowbinsize_in The number of pixels composing one array element in
the dimension that changes at the second-fastest rate.
fastbinsize_in The number of pixels composing one array element in
the dimension that changes at the fastest rate.
RETURN VALUE
Returns an error code on failure or 0 for success.
----------------------------------------------------------------------
2.5 F90 function interfaces
At the suggestion of W. Kabsch, Fortran 90/95 routines have been added
to CBFlib. As of this writing code has been written to allow the reading
of CBF_BYTE_OFFSET, CBF_PACKED and CBF_PACKED_V2 binary images. This
code has been gather into FCBlib (Fortran Crystallographic Binary
library) as lib/libfcb.
In general, most of the FCBlib functions return 0 for normal completion
and a non-zero value in case of an error. In a few cases, such as
FCB_ATOL_WCNT and FCB_NBLEN_ARRAY in order to conform to the conventions
for commonly used C-equivalent functions, the function return is the
value being computed.
For each function, an interface is given to be included in the
declarations of your Fortran 90/95 code. Some functions in FCBlIB are
not intended for external use and are subject to change:
FCB_UPDATE_JPA_POINTERS_I2, FCB_UPDATE_JPA_POINTERS_I4,
FCB_UPDATE_JPA_POINTERS_3D_I2, FCB_UPDATE_JPA_POINTERS_3D_I4 and
CNT2PIX. These names should not be used for user routines.
The functions involving reading of a CBF have been done strictly in
Fortran without the use of C code. This has required some compromises
and the use of direct access I/O. Rather than putting the buffer and its
control variables into COMMON these are passed as local arguments to
make the routines inherently 'threadsafe' in a parallel programming
environment. Note also, that a reading error could occur for the last
record if it does not fill a full block. The code is written to recover
from end-of-record and end-of-file errors, if possible. On many modern
system, no special action is required, but on some systems it may be
necessary to make use of the padding between the end of binary data and
the terminal MIME boundary marker in binary sections. To ensure maximum
portability of CBF files, a padding of 4095 bytes is recommended.
Existing files without padding can be converted to files with padding by
use of the new -p4 option for cif2cbf.
2.5.1 FCB_ATOL_WCNT
INTERFACE
INTEGER(8) FUNCTION FCB_ATOL_WCNT(ARRAY, N, CNT)
INTEGER(1),INTENT(IN):: ARRAY(N)
INTEGER, INTENT(IN):: N
INTEGER, INTENT(OUT):: CNT
END FUNCTION
END INTERFACE
FCB_ATOL_WCNT converts INTEGER(1) bytes in ARRAY of N bytes to an
INTEGER(8) value returned as the function value. The number of bytes of
ARRAY actually used before encountering a character not used to form the
number is returned in CNT.
The scan stops at the first byte in ARRAY that cannot be properly parsed
as part of the integer result.
ARGUMENTS
ARRAY The array of INTEGER(1) bytes to be scanned
N The INTEGER size of ARRAY
CNT The INTEGER size of the portion of ARRAY scanned.
RETURN VALUE
Returns the INTEGER(8) value derived from the characters ARRAY(1:CNT)
scanned.
----------------------------------------------------------------------
2.5.2 FCB_CI_STRNCMPARR
INTERFACE
INTEGER FUNCTION FCB_CI_STRNCMPARR(STRING>, ARRAY, N, LIMIT)
CHARACTER(LEN=*),INTENT(IN):: STRING>
INTEGER, INTENT(IN):: N, LIMIT
INTEGER(1), INTENT(IN):: ARRAY(N)
END FUNCTION
END INTERFACE
The function FCB_CI_STRNCMPARR compares up to LIMIT characters of
character string STRING and INTEGER(1) byte array ARRAY of dimension N
in a case-insensitive manner, returning 0 for a match.
ARGUMENTS
STRING A character string
ARRAY The array of INTEGER(1) bytes to be scanned
N The INTEGER size of ARRAY
N The INTEGER limit on the number of characters to consider in
the comparison
RETURN VALUE
Returns 0 if the string and array match, a non-zero value otherwise.
----------------------------------------------------------------------
2.5.3 FCB_EXIT_BINARY
INTERFACE
INTEGER FUNCTION FCB_EXIT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
PADDING )
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER(8),INTENT(IN) :: PADDING
END FUNCTION
END INTERFACE
The function FCB_EXIT_BINARY is used to skip from the end of a binary
section past any padding to the end of the text section that encloses
the binary section. The values of the arguments must be consistent with
those in the last call to FCB_NEXT_BINARY
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The last character (as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
PADDING The INTEGER(8) number of bytes of padding after the
binary data and before the closing MIME boundary.
RETURN VALUE
Returns 0 if the function is successful. Returns whatever non-zero error
value is reported by FCB_READ_LINE if a necessary next line cannot be
read.
SEE ALSO
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.4 FCB_NBLEN_ARRAY
INTERFACE
INTEGER FUNCTION FCB_NBLEN_ARRAY(ARRAY, ARRAYLEN)
INTEGER, INTENT(IN):: ARRAYLEN
INTEGER(1), INTENT(IN):: ARRAY(ARRAYLEN)
END FUNCTION
END INTERFACE
The function FCB_NBLEN_ARRAY returns the trimmed length of the
INTEGER(1) byte array ARRAY of dimension ARRAYLEN after removal of
trailing ASCII blanks, horizontal tabs (Z'09'), newlines (Z'0A') and
carriage returns (Z'0D'). The resulting length may be zero.
The INTEGER trimmed length is returned as the function value.
ARGUMENTS
ARRAY The array of bytes for which the trimmed length is
required.
ARRAYLEN The dimension of the array of bytes to be scanned.
RETURN VALUE
Returns the trimmed length of the array ARRAY.
----------------------------------------------------------------------
2.5.5 FCB_NEXT_BINARY
INTERFACE
INTEGER FUNCTION FCB_NEXT_BINARY(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC,&
BYTE_IN_FILE,REC_IN_FILE,BUFFER, &
ENCODING,SIZE,ID,DIGEST, &
COMPRESSION,BITS,VORZEICHEN,REELL,&
BYTEORDER,DIMOVER,DIM1,DIM2,DIM3, &
PADDING )
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(OUT) :: ENCODING
INTEGER, INTENT(OUT) :: SIZE !Binary size
INTEGER, INTENT(OUT) :: ID !Binary ID
CHARACTER(len=*),INTENT(OUT):: DIGEST !Message digest
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER, INTENT(OUT):: BITS,VORZEICHEN,REELL
CHARACTER(len=*),INTENT(OUT):: BYTEORDER
INTEGER(8), INTENT(OUT):: DIMOVER
INTEGER(8), INTENT(OUT):: DIM1
INTEGER(8), INTENT(OUT):: DIM2
INTEGER(8), INTENT(OUT):: DIM3
INTEGER(8), INTENT(OUT):: PADDING
END FUNCTION
END INTERFACE
The function FCB_NEXT_BINARY skips to the start of the next binary
section in the image file on unit TAPIN leaving the file positioned for
a subsequent read of the image data. The skip may prior to the text
field that contains the binary section. When the text filed is reached,
it will be scanned for a MIME boundary marker, and, if it is found the
subsequence MIME headers will be used to populate the arguments
ENCODING, SIZE, ID, DIGEST, COMPRESSION, BITS, VORZEICHEN,REELL,
BYTEORDER, DIMOVER, DIM1, DIM2,DIM3, PADDING.
The value returned in ENCODING is taken from the MIME header
Content-Transfer-Encoding as an INTEGER. It is returned as 0 if not
specified. The reported value is one of the integer values ENC_NONE
(Z'0001') for BINARY encoding, ENC_BASE64 (Z'0002') for BASE64 encoding,
ENC_BASE32K (Z'0004') for X-BASE32K encoding, ENC_QP (Z'0008') for
QUOTED-PRINTABLE encoding, ENC_BASE10 (Z'0010') for BASE10 encoding,
ENC_BASE16 (Z'0020') for BASE16 encoding or ENC_BASE8 (Z'0040') for
BASE8 encoding. At this time FCBlib only supports ENC_NONE BINARY
encoding.
The value returned in SIZE is taken from the MIME header X-Binary-Size
as an INTEGER. It is returned as 0 if not specified.
The value returned in ID is taken from the MIME header X-Binary-ID as an
INTEGER. It is returned as 0 if not specified.
The value returned in DIGEST is taken from the MIME header Content-MD5.
It is returned as a character string. If no digest is given, an empty
string is returned.
The value returned in COMPRESSION is taken from the MIME header
Content-Type in the conversions parameter. The reported value is one of
the INTEGER values CBF_CANONICAL (Z'0050'), CBF_PACKED (Z'0060'),
CBF_PACKED_V2 (Z'0090'), CBF_BYTE_OFFSET (Z'0070'), CBF_PREDICTOR
(Z'0080'), CBF_NONE (Z'0040'). Two flags may be combined with CBF_PACKED
or CBF_PACKED_V2: CBF_UNCORRELATED_SECTIONS (Z'0100') or CBF_FLAT_IMAGE
(Z'0200'). At this time FCBlib does not support CBF_PREDICTOR or
CBF_NONE compression.
The values returned in BITS, VORZEICHEN and REELL are the parameters of
the data types of the elements. These values are taken from the MIME
header X-Binary-Element-Type, which has values of the form "signed
BITS-bit integer", "unsigned BITS-bit integer", "signed BITS-bit real
IEEE" or "signed BITS-bit complex IEEE". If no value is given, REELL is
reported as -1. If the value in one of the integer types, REELL is
reported as 0. If the value is one of the real or complex types, REELL
is reported as 1. In the current release of FCBlib only the integer
types for BITS equal to 16 or 32 are supported.
The value returned in BYTEORDER is the byte order of the data in the
image file as reported in the MIME header. The value, if specified, will
be either the character string "LITTLE_ENDIAN" or the character string
"BIG_ENDIAN". If no byte order is specified, "LITTLE_ENDIAN" is
reported. This value is taken from the MIME header
X-Binary-Element-Byte-Order. As of this writing, CBFlib will not
generate "BIG_ENDIAN" byte-order files. However, both CBFlib and FCBlib
read "LITTLE_ENDIAN" byte-order files, even on big-endian machines.
The value returned in DIMOVER is the overall number of elements in the
image array, if specified, or zero, if not specified. This value is
taken from the MIME header X-Binary-Number-of-Elements. The values
returned in DIM1, DIM2 and DIM3 are the sizes of the fastest changing,
second fastest changing and third fastest changing dimensions of the
array, if specified, or zero, if not specified. These values are taken
from the MIME header X-Binary-Size-Fastest-Dimension,
X-Binary-Size-Second-Dimension and X-Binary-Size-Third-Dimension
respectively.
The value returned in PADDING is the size of the post-data padding, if
any, if specified or zero, if not specified. The value is given as a
count of octets. This value is taken from the MIME header
X-Binary-Size-Padding.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The last character (as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
ENCODING INTEGER type of encoding for the binary section as
reported in the MIME header.
ID INTEGER binary identifier as reported in the MIME
header.
SIZE INTEGER size of compressed binary section as
reported in the MIME header.
DIGEST The MD5 message digest as reported in the MIME
header.
COMPRESSION INTEGER compression method as reported in the MIME
header.
BITS INTEGER number of bits in each element as reported
in the MIME header.
VORZEICHEN INTEGER flag for signed or unsigned elements as
reported in the MIME header. Set to 1 if the elements
can be read as signed values, 0 otherwise.
REELL INTEGER flag for real elements as reported in the
MIME header. Set to 1 if the elements can be read as
REAL
BYTEORDER The byte order as reported in the MIME header.
DIM1 Pointer to the destination fastest dimension.
DIM2 Pointer to the destination second fastest
dimension.
DIM3 Pointer to the destination third fastest dimension.
PADDING Pointer to the destination padding size.
RETURN VALUE
Returns 0 if the function is successful. SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.6 FCB_OPEN_CIFIN
INTERFACE
INTEGER FUNCTION FCB_OPEN_CIFIN(FILNAM,TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER)
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,FCB_BYTES_IN_REC
INTEGER(1), INTENT(OUT):: LAST_CHAR
INTEGER, INTENT(OUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER(1), INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER FCB_RECORD_SIZE
END FUNCTION
END INTERFACE
The function FCB_OPEN_CIFIN opens the CBF image file given by the file
name in the character string FILNAM on the logical unit TAPIN. The
calling routine must provide an INTEGER(1) byte buffer BUFFER of some
appropriate INTEGER size FCB_BYTES_IN_REC. The size must be chosen to
suit the machine, but in most cases, 4096 will work. The values returned
in LAST_CHAR, BYTE_IN_FILE, and REC_IN_FILE are for use in subsequent
FCBlib I/O routines.
The image file will be checked for the initial characters "###CBF: ". If
there is no match the error value CBF_FILEREAD is returned.
ARGUMENTS
FILNAM The character string name of the image file to be
opened.
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The last character (as an INTEGER(1) byte) read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
RETURN VALUE
Returns 0 if the function is successful. SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.7 FCB_PACKED: FCB_DECOMPRESS_PACKED_I2, FCB_DECOMPRESS_PACKED_I4,
FCB_DECOMPRESS_PACKED_3D_I2, FCB_DECOMPRESS_PACKED_3D_I4
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_I2 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_I4 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_3D_I2 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_DECOMPRESS_PACKED_3D_I4 (ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN, COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
The functions FCB_DECOMPRESS_PACKED_I2, FCB_DECOMPRESS_PACKED_I4,
FCB_DECOMPRESS_PACKED_3D_I2 and FCB_DECOMPRESS_PACKED_3D_I4, decompress
images compress according the the CBF_PACKED or CBF_PACKED_V2
compression described in section 3.3.2 on J. P. Abrahams CCP4 packed
compression.
The relevant function should be called immediately after a call to
FCB_NEXT_BINARY, using the values returned by FCB_NEXT_BINARY to select
the appropriate version of the function.
ARGUMENTS
ARRAY The array to receive the image
NELEM The INTEGER(8) number of elements to be read
NELEM_READ The INTEGER(8) returned value of the number of
elements actually read
ELSIGN The INTEGER value of the flag for signed (1) OR
unsigned (0) data
COMPRESSION The compression of the image
DIM1 The INTEGER(8) value of the fastest dimension of
ARRAY
DIM2 The INTEGER(8) value of the second fastest
dimension
DIM3 The INTEGER(8) value of the third fastest dimension
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.8 FCB_READ_BITS
INTERFACE
INTEGER FUNCTION FCB_READ_BITS(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,BCOUNT,BBYTE, &
BITCOUNT,IINT,LINT)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER, INTENT(INOUT):: BCOUNT
INTEGER(1),INTENT(INOUT):: BBYTE
INTEGER, INTENT(IN):: BITCOUNT
INTEGER, INTENT(IN):: LINT
INTEGER(4), INTENT(OUT):: IINT(LINT)
END FUNCTION
END INTERFACE
The function FCB_READ_BITS gets the integer value starting at
BYTE_IN_FILE from file TAPIN continuing through BITCOUNT bits, with sign
extension. BYTE_IN_FILE is left at the entry value and not incremented.
The resulting, sign-extended integer value is stored in the INTEGER(4)
array IINT of dimension LINT with the least significant portion in
IINT(1).
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
BCOUNT The INTEGER count of bits remaining unused from the
last call to FCB_READ_BITS.
BBYTE The INTEGER(1) byte containing the unused bits from
the last call to FCB_READ_BITS.
BITCOUNT The INTEGER count of the number of bits to be
extracted from the image file.
IINT The INTEGER(4) array into which to store the value
extracted from the image file.
LINT The INTEGER length of the array IINT.
RETURN VALUE
Returns 0 if the function is successful. Because of the use of direct
access I/O in blocks of size FCB_BYTES_IN_REC the precise location of
the end of file may not be detected.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.9 FCB_READ_BYTE
INTERFACE
INTEGER FUNCTION FCB_READ_BYTE(TAPIN,FCB_BYTES_IN_REC,BUFFER, &
REC_IN_FILE,BYTE_IN_FILE,IBYTE)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: IBYTE
END FUNCTION
END INTERFACE
The function FCB_READ_BYTE reads the byte at the position BYTE_IN_FILE
in the image file TAPIN. The first byte in the file is at BYTE_IN_FILE =
1. BYTE_IN_FILE should be set to the desired value before the call to
the function and is not incremented within the function.
The function attempts to suppress the error caused by a read of a short
last record, and in most systems cannot determine the exact location of
the end of the image file, returning zero bytes until the equivalent of
a full final record has been read.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
IBYTE The INTEGER(1) byte found in the image file at the
byte position BYTE_IN_FILE.
RETURN VALUE
Returns 0 if the function is successful. Because of the use of direct
access I/O in blocks of size FCB_BYTES_IN_REC the precise location of
the end of file may not be detected.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.9 FCB_READ_BITS
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.10 FCB_READ_IMAGE_I2, FCB_READ_IMAGE_I4, FCB_READ_IMAGE_3D_I2,
FCB_READ_IMAGE_3D_I4
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_I2(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_I4(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_3D_I2(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(2), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
INTERFACE
INTEGER FUNCTION FCB_READ_IMAGE_3D_I4(ARRAY,NELEM,NELEM_READ, &
ELSIGN, COMPRESSION, DIM1, DIM2, DIM3, &
PADDING,TAPIN,FCB_BYTES_IN_REC,BYTE_IN_FILE, &
REC_IN_FILE,BUFFER)
INTEGER(4), INTENT(OUT):: ARRAY(DIM1,DIM2,DIM3)
INTEGER(8), INTENT(OUT):: NELEM_READ
INTEGER(8), INTENT(IN):: NELEM
INTEGER, INTENT(IN):: ELSIGN
INTEGER, INTENT(OUT):: COMPRESSION
INTEGER(8), INTENT(IN):: DIM1,DIM2,DIM3
INTEGER(8), INTENT(OUT):: PADDING
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC
INTEGER, INTENT(INOUT):: REC_IN_FILE,BYTE_IN_FILE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC)
END FUNCTION
END INTERFACE
The function FCB_READ_IMAGE_I2 reads a 16-bit twos complement INTEGER(2)
2D image. The function FCB_READ_IMAGE_I4 read a 32-bit twos complement
INTEGER(4) 2D image. The function FCB_READ_IMAGE_3D_I2 reads a 16-bit
twos complement INTEGER(2) 3D image. The function FCB_READ_IMAGE_3D_I4
reads a 32-bit twos complement INTEGER(4) 3D image. In each case the
image is compressed either by a BYTE_OFFSET algorithm by W. Kabsch based
on a proposal by A. Hammersley or by a PACKED algorithm by J. P.
Abrahams as used in CCP4, with modifications by P. Ellis and H. J.
Bernstein.
The relevant function automatically first calls FCB_NEXT_BINARY to skip
to the next binary section and then starts to read. An error return will
result if the parameters of this call are inconsistent with the values
in MIME header.
ARGUMENTS
ARRAY The array to receive the image
NELEM The INTEGER(8) number of elements to be read
NELEM_READ The INTEGER(8) returned value of the number of
elements actually read
ELSIGN The INTEGER value of the flag for signed (1) OR
unsigned (0) data
COMPRESSION The actual compression of the image
DIM1 The INTEGER(8) value of the fastest dimension of
ARRAY
DIM2 The INTEGER(8) value of the second fastest
dimension
DIM3 The INTEGER(8) value of the third fastest dimension
TAPIN The INTEGER Fortran device unit number assigned to
image file.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.7 FCB_DECOMPRESS: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
2.5.9 FCB_READ_BYTE
2.5.11 FCB_READ_LINE
----------------------------------------------------------------------
2.5.11 FCB_READ_LINE
INTERFACE
INTEGER FUNCTION FCB_READ_LINE(TAPIN,LAST_CHAR,FCB_BYTES_IN_REC, &
BYTE_IN_FILE,REC_IN_FILE,BUFFER,LINE,N,LINELEN)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC,N
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE
INTEGER, INTENT(OUT):: LINELEN
INTEGER(1),INTENT(INOUT):: LAST_CHAR,BUFFER,(FCB_BYTES_IN_REC)
INTEGER(1), INTENT(OUT):: LINE(N)
END FUNCTION
END INTERFACE
The function FCB_READ_LINE reads successive bytes into the INTEGER(1)
byte array LINE of dimension N), stopping at N bytes or the first error
or the first CR (Z'0D') or LF (Z'0A'), whichever comes first. It
discards an LF after a CR. The variable LAST_CHAR is checked for the
last character from the previous line to make this determination.
The actual number of bytes read into the line, not including any
terminal CR or LF is stored in LINELEN.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The INTEGER(1) byte holding the ASCII value of the
last character read for each line read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN.
LINE The INTEGER(1) array of length N to hold the line
to be read from TAPIN.
N The INTEGER dimension of LINE.
LINELEN The INTEGER number of characters read into LINE.
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.7 FCB_DECOMPRESS: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
2.5.9 FCB_READ_BYTE
2.5.12 FCB_READ_XDS_I2
INTERFACE
INTEGER FUNCTION FCB_READ_XDS_I2(FILNAM,TAPIN,NX,NY,IFRAME,JFRAME)
CHARACTER(len=*),INTENT(IN) :: FILNAM
INTEGER, INTENT(IN) :: TAPIN,NX,NY
INTEGER(2), INTENT(OUT):: IFRAME(NX*NY)
INTEGER(4), INTENT(OUT):: JFRAME(NX,NY)
END FUNCTION
END INTERFACE
The function FCB_READ_XDS_I2 read a 32-bit integer twos complement image
into a 16-bit INTEGER(2) XDS image using the CBF_BYTE_OFFSET, CBF_PACKED
or CBF_PACKED_V2 compressions for the 32-bit data. The BYTE_OFFSET
algorithm is a variant of the September 2006 version by W. Kabsch which
was based on a suggestion by A. Hammersley and which was further
modified by H. Bernstein.
The file named FILNAM is opened on the logical unit TAPIN and
FCB_NEXT_BINARY is used to skip to the next binary image. The binary
image is then decompressed to produce an XDS 16-bit integer image array
IFRAME which is NX by NY. The dimensions must agree with the dimensions
specified in MIME header.
The conversion from a 32-bit integer I32 to 16-bit XDS pixel I16 is done
as per W. Kabsch as follows: The value I32 is limited to the range -1023
=< I32 =< 1048576. If I32 is outside that range it is truncated to the
closer boundary. The generate I16, the 16-bit result, if I32 > 32767, it
is divided by 32 (producing a number between 1024 and 32768), and then
negated (producing a number between -1024 and -32768).
For CBF_BYTE_OFFSET this conversion can be done on the fly directly into
the target array IFRAME, but for the CBF_PACKED or CBF_PACKED_V2, the
full 32 bit precision is needed during the decompression, forcing the
use of an intermediate INTEGER(4) array JFRAME to hold the 32-bit image
in that case.
The image file is closed after reading one image.
ARGUMENTS
FILNAM The character string name of the image file to be opened.
TAPIN The INTEGER Fortran device unit number assigned to image
file.
NX The INTEGER fast dimension of the image array.
NY The INTEGER slow dimension of the image array.
IFRAME The INTEGER(2) XDS image array.
JFRAME The INTEGER(4) 32-bit image scratch array needed for
CBF_PACKED or CBF_PACKED_V2 images.
RETURN VALUE
Returns 0 if the function is successful, CBF_FORMAT (=1) if it cannot
handle this CBF format (not implemented), -1 if it cannot determine
endian architecture of this machine, -2: if it cannot open the image
file, -3: if it finds the wrong image format and -4 if it cannot read
the image.
----------------------------------------------------------------------
2.5.13 FCB_SKIP_WHITESPACE
INTERFACE
INTEGER FUNCTION FCB_SKIP_WHITESPACE(TAPIN,LAST_CHAR, &
FCB_BYTES_IN_REC,BYTE_IN_FILE,REC_IN_FILE,BUFFER,&
LINE,N,LINELEN,ICUR,FRESH_LINE)
INTEGER, INTENT(IN):: TAPIN,FCB_BYTES_IN_REC,N
INTEGER, INTENT(INOUT):: BYTE_IN_FILE,REC_IN_FILE,LINELEN,ICUR, &
FRESH_LINE
INTEGER(1),INTENT(INOUT):: BUFFER(FCB_BYTES_IN_REC),LINE(N), &
LAST_CHAR
END INTERFACE
The function FCB_SKIP_WHITESPACE skips forward on the current INTEGER(1)
byte array LINE of size N with valid data in LINE(1:LINELEN) from the
current position ICUR moving over MIME header whitespace and comments,
reading new lines into LINE if needed. The flag FRESH_LINE indicates
that a fresh line should be read on entry.
ARGUMENTS
TAPIN The INTEGER Fortran device unit number assigned to
image file.
LAST_CHAR The INTEGER(1) byte holding the ASCII value of the
last character read for each line read.
FCB_BYTES_IN_REC The INTEGER number of bytes in a record.
BYTE_IN_FILE The INTEGER byte (counting from 1) of the byte to
read.
REC_IN_FILE The INTEGER record number (counting from 1) of next
record to read.
BUFFER The INTEGER(1) array of length FCB_BYTES_IN_REC to
hold the appropriate record from TAPIN.
LINE The INTEGER(1) array of length N to hold the line
to be read from TAPIN.
N The INTEGER dimension of LINE.
LINELEN The INTEGER number of characters read into LINE.
ICUR The INTEGER position within the line.
FRESH_LINE The INTEGER flag that a fresh line is needed.
RETURN VALUE
Returns 0 if the function is successful.
SEE ALSO
2.5.3 FCB_EXIT_BINARY
2.5.5 FCB_NEXT_BINARY
2.5.6 FCB_OPEN_CIFIN
2.5.7 FCB_DECOMPRESS: FCB_DECOMPRESS_PACKED_I2,
FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2,
FCB_DECOMPRESS_PACKED_3D_I4
2.5.9 FCB_READ_BYTE
----------------------------------------------------------------------
3. File format
3.1 General description
With the exception of the binary sections, a CBF file is an mmCIF-format
ASCII file, so a CBF file with no binary sections is a CIF file. An
imgCIF file has any binary sections encoded as CIF-format ASCII strings
and is a CIF file whether or not it contains binary sections. In most
cases, CBFlib can also be used to access normal CIF files as well as CBF
and imgCIF files.
3.2 Format of the binary sections
Before getting to the binary data itself, there are some preliminaries
to allow a smooth transition from the conventions of CIF to those of raw
or encoded streams of "octets" (8-bit bytes). The binary data is given
as the essential part of a specially formatted semicolon-delimited CIF
multi-line text string. This text string is the value associated with
the tag "_array_data.data".
The specific format of the binary sections differs between an imgCIF and
a CBF file.
3.2.1 Format of imgCIF binary sections
Each binary section is encoded as a semicolon-delimited string. Within
the text string, the conventions developed for transmitting email
messages including binary attachments are followed. There is secondary
ASCII header information, formatted as Multipurpose Internet Mail
Extensions (MIME) headers (see RFCs 2045-49 by Freed, et al.). The
boundary marker for the beginning of all this is the special string
--CIF-BINARY-FORMAT-SECTION--
at the beginning of a line. The initial "--" says that this is a MIME
boundary. We cannot put "###" in front of it and conform to MIME
conventions. Immediately after the boundary marker are MIME headers,
describing some useful information we will need to process the binary
section. MIME headers can appear in different orders, and can be very
confusing (look at the raw contents of a email message with
attachments), but there is only one header which is has to be understood
to process an imgCIF: "Content-Transfer-Encoding". If the value given on
this header is "BINARY", this is a CBF and the data will be presented as
raw binary, containing a count (in the header described in 3.2.2 Format
of CBF binary sections) so that we'll know when to start looking for
more information.
If the value given for "Content-Transfer-Encoding" is one of the real
encodings: "BASE64", "QUOTED-PRINTABLE", "X-BASE8", "X-BASE10" or
"X-BASE16", the file is an imgCIF, and we'll need some other headers to
process the encoded binary data properly. It is a good practice to give
headers in all cases. The meanings of various encodings is given in the
CBF extensions dictionary, cif_img_1.5.4.dic, as one html file, or as
separate pages for each defintion.
For certain compressions (e.g. CBF_PACKED) MIME headers are essential to
determine the parameters of the compression. The full list of MIME
headers recognized by and generated by CBFlib is:
* Content-Type:
* Content-Transfer-Encoding:
* Content-MD5:
* X-Binary-Size:
* X-Binary-ID:
* X-Binary-Element-Type:
* X-Binary-Element-Byte-Order:
* X-Binary-Number-of-Elements:
* X-Binary-Size-Fastest-Dimension:
* X-Binary-Size-Second-Dimension:
* X-Binary-Size-Third-Dimension:
* X-Binary-Size-Padding:
* Content-Type:
The "Content-Type" header tells us what sort of data we
have (currently always "application/octet-stream" for a
miscellaneous stream of binary data) and, optionally, the
conversions that were applied to the original data. The default is
to compress the data with the "CBF-PACKED" algorithm. The
Content-Type may be any of the discrete types permitted in RFC 2045;
'application/octet-stream' is recommended. If an octet stream was
compressed, the compression should be specified by the parameter
'conversions="X-CBF_PACKED"' or the parameter
'conversions="X-CBF_PACKED_V2"' or the parameter
'conversions="X-CBF_CANONICAL"' or the parameter
'conversions="X-CBF_BYTE_OFFSET"'
If the parameter 'conversions="X-CBF_PACKED"' or
'conversions="X-CBF_PACKED_V2"' is given it may be further modified
with the parameters '"uncorrelated_sections"' or '"flat"'
If the '"uncorrelated_sections"' parameter is given, each section
will be compressed without using the prior section for averaging. If
the '"flat"' parameter is given, each the image will be treated as
one long row.
* Content-Transfer-Encoding:
The "Content-Transfer-Encoding" may be 'BASE64', 'Quoted-Printable',
'X-BASE8', 'X-BASE10', 'X-BASE16' or 'X-BASE32K', for an imgCIF or
'BINARY' for a CBF. The octal, decimal and hexadecimal transfer
encodings are provided for convenience in debugging and are not
recommended for archiving and data interchange.
In a CIF, one of the parameters 'charset=us-ascii', 'charset=utf-8'
or 'charset=utf-16' may be used on the Content-Transfer-Encoding to
specify the character set used for the external presentation of the
encoded data. If no charset parameter is given, the character set of
the enclosing CIF is assumed. In any case, if a BOM flag is detected
(FE FF for big-endian UTF-16, FF FE for little-endian UTF-16 or EF
BB BF for UTF-8) is detected, the indicated charset will be assumed
until the end of the encoded data or the detection of a different
BOM. The charset of the Content-Transfer-Encoding is not the
character set of the encoded data, only the character set of the
presentation of the encoded data and should be respecified for each
distinct STAR string.
In an imgCIF file, the encoded binary data begins after the empty
line terminating the header. In an imgCIF file, the encoded binary
data ends with the terminating boundary delimiter
'\n--CIF-BINARY-FORMAT-SECTION----' in the currently effective
charset or with the '\n; ' that terminates the STAR string.
In a CBF, the raw binary data begins after an empty line terminating
the header and after the sequence:
Octet Hex Decimal Purpose
0 0C 12 (ctrl-L) Page break
1 1A 26 (ctrl-Z) Stop listings in MS-DOS
2 04 04 (Ctrl-D) Stop listings in UNIX
3 D5 213 Binary section begins
None of these octets are included in the calculation of the message
size or in the calculation of the message digest.
* Content-MD5:
An MD5 message digest may, optionally, be used. The 'RSA Data
Security, Inc. MD5 Message-Digest Algorithm' should be used. No
portion of the header is included in the calculation of the message
digest. The optional "Content-MD5" header provides a much more
sophisticated check on the integrity of the binary data than size
checks alone can provide.
* X-Binary-Size:
The "X-Binary-Size" header specifies the size of the equivalent
binary data in octets. This is the size after any compressions, but
before any ascii encodings. This is useful in making a simple check
for a missing portion of this file. The 8 bytes for the Compression
type (see below) are not counted in this field, so the value of
"X-Binary-Size" is 8 less than the quantity in bytes 12-19 of the
raw binary data ( 3.2.2 Format of CBF binary sections).
* X-Binary-ID:
The "X-Binary-ID" header should contain the same value as was given
for "_array_data.binary_id".
* X-Binary-Element-Type:
The "X-Binary-Element-Type" header specifies the type of binary data
in the octets, using the same descriptive phrases as in
_array_structure.encoding_type. The default value is 'unsigned
32-bit integer'.
* X-Binary-Element-Byte-Order:
The "X-Binary-Element-Byte-Order" can specify either '"BIG_ENDIAN"'
or '"LITTLE_ENDIAN"' byte order of the image data. CBFlib only
writes '"LITTLE_ENDIAN"', and in general can only process
LITTLE_ENDIAN even on machines that are BIG_ENDIAN.
* X-Binary-Number-of-Elements:
The "X-Binary-Number-of-Elements" specifies the number of elements
(not the number of octets) in the decompressed, decoded image.
* X-Binary-Size-Fastest-Dimension:
The optional "X-Binary-Size-Fastest-Dimension" specifies the number
of elements (not the number of octets) in one row of the fastest
changing dimension of the binary data array. This information must
be in the MIME header for proper operation of some of the
decompression algorithms.
* X-Binary-Size-Second-Dimension:
The optional "X-Binary-Size-Second-Dimension" specifies the number
of elements (not the number of octets) in one column of the
second-fastest changing dimension of the binary data array. This
information must be in the MIME header for proper operation of some
of the decompression algorithms.
* X-Binary-Size-Third-Dimension:
The optional "X-Binary-Size-Third-Dimension" specifies the number of
sections for the third-fastest changing dimension of the binary data
array.
* X-Binary-Size-Padding:
The optional "X-Binary-Size-Padding" specifies the size in octets of
an optional padding after the binary array data and before the
closing flags for a binary section. CBFlib always writes this
padding as zeros, but this information should be in the MIME header
for a binary section that uses padding, especially if non-zero
padding is used.
A blank line separator immediately precedes the start of the encoded
binary data. Blank spaces may be added prior to the preceding "line
separator" if desired (e.g. to force word or block alignment).
Because CBFLIB may jump forward in the file from the MIME header, the
length of encoded data cannot be greater than the value defined by
"X-Binary-Size" (except when "X-Binary-Size" is zero, which means that
the size is unknown), unless "X-Binary-Size-Padding" is specified to
allow for the padding. At exactly the byte following the full binary
section as defined by the length and padding values is the end of binary
section identifier. This consists of the line-termination sequence
followed by:
--CIF-BINARY-FORMAT-SECTION----
;
with each of these lines followed by a line-termination sequence. This
brings us back into a normal CIF environment. This identifier is, in a
sense, redundant because the binary data length value tells the a
program how many bytes to jump over to the end of the binary data. This
redundancy has been deliberately added for error checking, and for
possible file recovery in the case of a corrupted file and this
identifier must be present at the end of every block of binary data.
3.2.2 Format of CBF binary sections
In a CBF file, each binary section is encoded as a ;-delimited string,
starting with an arbitrary number of pure-ASCII characters.
Note: For historical reasons, CIFlib has the option of writing simple
header and footer sections: "START OF BINARY SECTION" at the start of a
binary section and "END OF BINARY SECTION" at the end of a binary
section, or writing MIME-type header and footer sections (3.2.1 Format
of imgCIF binary sections). If the simple header is used, the actual
ASCII text is ignored when the binary section is read. Use of the simple
binary header is deprecated.
The MIME header is recommended.
Between the ASCII header and the actual CBF binary data is a series of
bytes ("octets") to try to stop the listing of the header, bytes which
define the binary identifier which should match the "binary_id" defined
in the header, and bytes which define the length of the binary section.
Octet Hex Decimal Purpose
1 0C 12 (ctrl-L) End of Page
2 1A 26 (ctrl-Z) Stop listings in MS-DOS
3 04 04 (Ctrl-D) Stop listings in UNIX
4 D5 213 Binary section begins
5..5+n-1 Binary data (n octets)
NOTE: When a MIME header is used, only bytes 5 through 5+n-1 are
considered in computing the size and the message digest, and only these
bytes are encoded for the equivalent imgCIF file using the indicated
Content-Transfer-Encoding.
If no MIME header has been requested (a deprecated use), then bytes 5
through 28 are used for three 8-byte words to hold the binary_id, the
size and the compression type:
5..12 Binary Section Identifier
(See _array_data.binary_id)
64-bit, little endian
13..20 The size (n) of the
binary section in octets
(i.e. the offset from octet
29 to the first byte following
the data)
21..28 Compression type:
CBF_NONE 0x0040 (64)
CBF_CANONICAL 0x0050 (80)
CBF_PACKED 0x0060 (96)
CBF_BYTE_OFFSET 0x0070 (112)
CBF_PREDICTOR 0x0080 (128)
...
The binary data then follows in bytes 29 through 29+n-1.
The binary characters serve specific purposes:
o The Control-L (from-feed) will terminate printing of the current
page on most operating systems.
o The Control-Z will stop the listing of the file on MS-DOS type
operating systems.
o The Control-D will stop the listing of the file on Unix type
operating systems.
o The unsigned byte value 213 (decimal) is binary 11010101. (Octal
325, and hexadecimal D5). This has the eighth bit set so can be used
for error checking on 7-bit transmission. It is also asymmetric, but
with the first bit also set in the case that the bit order could be
reversed (which is not a known concern).
o (The carriage return, line-feed pair before the START_OF_BIN and
other lines can also be used to check that the file has not been
corrupted e.g. by being sent by ftp in ASCII mode.)
At present four compression schemes are implemented are defined:
CBF_NONE (for no compression), CBF_CANONICAL (for and entropy-coding
scheme based on the canonical-code algorithm described by Moffat, et
al. (International Journal of High Speed Electronics and Systems,
Vol 8, No 1 (1997) 179-231)), CBF_PACKED or CBF_PACKED_V2 for J. P.
Abrahams CCP4-style packing schemes and CBF_BYTE_OFFSET for a simple
byte_offset compression scheme.. Other compression schemes will be
added to this list in the future.
For historical reasons, CBFlib can read or write a binary string without
a MIME header. The structure of a binary string with simple headers is:
Byte ASCII Decimal Description
symbol value
1 ; 59 Initial ; delimiter
2 carriage-return 13
3 line-feed 10 The CBF new-line code is
carriage-return, line-feed
4 S 83
5 T 84
6 A 65
7 R 83
8 T 84
9 32
10 O 79
11 F 70
12 32
13 B 66
14 I 73
15 N 78
16 A 65
17 R 83
18 Y 89
19 32
20 S 83
21 E 69
22 C 67
23 T 84
24 I 73
25 O 79
26 N 78
27 carriage-return 13
28 line-feed 10
29 form-feed 12
30 substitute 26 Stop the listing of the file
in MS-DOS
31 end-of-transmission 4 Stop the listing of the file
in unix
32 213 First non-ASCII value
33 .. 40 Binary section identifier
(64-bit little-endien)
41 .. 48 Offset from byte 57 to the
first ASCII character
following the binary data
49 .. 56 Compression type
57 .. 57 + n-1 Binary data (nbytes)
57 + n carriage-return 13
58 + n line-feed 10
59 + n E 69
60 + n N 78
61 + n D 68
62 + n 32
63 + n O 79
64 + n F 70
65 + n 32
66 + n B 66
67 + n I 73
68 + n N 78
69 + n A 65
70 + n R 83
71 + n Y 89
72 + n 32
73 + n S 83
74 + n E 69
75 + n C 67
76 + n T 84
77 + n I 73
78 + n O 79
79 + n N 78
80 + n carriage-return 13
81 + n line-feed 10
82 + n ; 59 Final ; delimiter
3.3 Compression schemes
Two schemes for lossless compression of integer arrays (such as images)
have been implemented in this version of CBFlib:
1. An entropy-encoding scheme using canonical coding
2. A CCP4-style packing scheme.
Both encode the difference (or error) between the current element in the
array and the prior element. Parameters required for more sophisticated
predictors have been included in the compression functions and will be
used in a future version of the library.
3.3.1 Canonical-code compression
The canonical-code compression scheme encodes errors in two ways:
directly or indirectly. Errors are coded directly using a symbol
corresponding to the error value. Errors are coded indirectly using a
symbol for the number of bits in the (signed) error, followed by the
error iteslf.
At the start of the compression, CBFlib constructs a table containing a
set of symbols, one for each of the 2^n direct codes from -2^(n-1) ..
2^(n-1)-1, one for a stop code, and one for each of the maxbits -n
indirect codes, where n is chosen at compress time and maxbits is the
maximum number of bits in an error. CBFlib then assigns to each symbol a
bit-code, using a shorter bit code for the more common symbols and a
longer bit code for the less common symbols. The bit-code lengths are
calculated using a Huffman-type algorithm, and the actual bit-codes are
constructed using the canonical-code algorithm described by Moffat, et
al. (International Journal of High Speed Electronics and Systems, Vol 8,
No 1 (1997) 179-231).
The structure of the compressed data is:
Byte Value
1 .. 8 Number of elements (64-bit
little-endian number)
9 .. 16 Minimum element
17 .. 24 Maximum element
25 .. 32 (reserved for future use)
33 Number of bits directly coded, n
34 Maximum number of bits encoded, maxbits
35 .. 35+2^n-1 Number of bits in each direct code
35+2^n Number of bits in the stop code
35+2^n+1 .. 35+2^n+maxbits-n Number of bits in each indirect code
35+2^n+maxbits-n+1 .. Coded data
3.3.2 CCP4-style compression
Starting with CBFlib 0.7.7, CBFlib supports three variations on
CCP4-style compression: the "flat" version supported in versions of
CBFlib prior to release 0.7.7, as well as both version 1 and version 2
of J. P. Abrahams "pack_c" compression.
The CBF_PACKED and CBF_PACKED_V2 compression and decompression code
incorporated in CBFlib is derived in large part from the J. P. Abrahams
pack_c.c compression code in CCP4. This code is incorporated in CBFlib
under the GPL and the LGPL with both the permission Jan Pieter Abrahams,
the original author of pack_c.c (email from Jan Pieter Abrahams of 15
January 2007) and of the CCP4 project (email from Martyn Winn on 12
January 2007). The cooperation of J. P. Abrahams and of the CCP4 project
is gratefully acknowledged.
The basis for all three versions is a scheme to pack offsets
(differences from a base value) into a small-endian bit stream. The
stream is organized into blocks. Each block begins with a header of 6
bits in the flat packed version and version 1 of J. P. Abrahams
compression, and 7 bits in version 2 of J. P. Abrahams compression. The
header gives the number of offsets that follow and the number of bits in
each offset. Each offset is a signed, 2's complement integer.
The first 3 bits in the header gives the logarithm base 2 of the numer
of offsets that follow the header. For example, if a header has a zero
in bits, only one offset follows the header. If those same bits contain
the number n, the number of offsets in the block is 2n.
The following 3 bits (flat and version 1) or 4 bits (version 2) contains
a number giving an index into a table of bit-lengths for the offsets.
All offsets in a given block are of the same length.
Bits 3 .. 5 (flat and version 1) or bits 3 .. 6 (version 2) encode the
number of bits in each offset as follows:
Value in Number of bits Number of bits
bits 3 .. 5 in each V1 offset in each V2 offset
0 0 0
1 4 3
2 5 4
3 6 5
4 7 6
5 8 7
6 16 8
7 max 9
8 10
9 11
10 12
11 13
12 14
13 15
14 16
15 max
The value "max" is determined by the compression version and the element
size. If the compression used is "flat", then "max" is 65. If the
compression is version 1 or version 2 of the JPA compression, then "max"
is the number of bits in each element, i.e. 8, 16, 32 or 64 bits.
The major difference between the three variants of packed compression is
the choice of the base value from which the offset is measured. In all
cases the first offset is measured from zero, i.e. the first offset is
the value of the first pixel of the image. If "flat" is chosen or if the
dimensions of the data array are not given, then the remaining offset
are measure against the prior value, making it similar in approach to
the "byte offset" compression described in section 3.3.3 Byte offset
compression, but with a more efficient representation of the offsets.
In version 1 and version 2 of the J. P. Abrahams compression, the
offsets are measured against an average of earlier pixels. If there is
only one row only the prior pxiel is used, starting with the same
offsets for that row as for "flat". After the first row, three pixels
from the prior row are used in addition to using the immediately prior
pixel. If there are multiple sections, and the sections are marked as
correlated, after the first section, 4 pixels from the prior section are
included in the average. The CBFlib code differs from the pack_c code in
the handling of the beginnings and ends of rows and sections. The pack_c
code will use pixels from the other side of the image in doing the
averaging. The CBFlib code drops pixels from the other side of the image
from the pool. The details follow.
After dealing with the special case of the first pixel, The algorithm
uses an array of pointers, trail_char_data. The assignment of pixels to
the pool to be averaged begins with trail_char_data[0] points to the
pixel immediately prior to the next pixel to be processed, either in the
same row (fastest index) or, at the end of the prior row if the next
data element to be processed is at the end of a row. The location of the
pixel pointed to by trail_char_data[0] is used to compute the locations
of the other pixels in the pool. It will be dropped from the pool before
averaging if it is on the opposite side of the image. The pool will
consist of 1, 2, 4 or 8 pixels.
Assume ndim1, ndim2, ndim3 are the indices of the same pixel as
trail_char_data[0] points to. These indices are incremented to be the
indices of the next pixel to be processed before populating
trail_char_data.
On exit, trail_char_data[0 .. 7] will have been populated with pointers
to the pixels to be used in forming the average. Pixels that will not be
used will be set to NULL. Note that trail_char_data[0] may be set to
NULL.
If we mark the next element to be processed with a "*" and the entries
in trail_char_data with their array indices 0 .. 7, the possible
patterns of settings in the general case are:
current section:
- - - - 0 * - - - -
- - - - 3 2 1 - - -
- - - - - - - - - -
prior section:
- - - - - 4 - - - -
- - - - 7 6 5 - - -
- - - - - - - - - -
If there is no prior section (i.e. ndim3 is 0, or the
CBF_UNCORRELATED_SECTIONS flag is set to indicate discontinuous
sections), the values for trail_char_data[4 .. 7] will all be NULL. When
there is a prior section, trail_char_data[5..7] are pointers to the
pixels immediately below the elements pointed to by
trail_char_data[1..3], except trail_char_data[4] is one element further
along its row to be directly below the next element to be processed.
The first element of the first row of the first section is a special
case, with no averaging.
In the first row of the first section (ndim2 == 0, and ndim3 == 0),
after the first element (ndim1 > 0), only trail_char_data[0] is used
current section:
- - - - 0 * - - - -
For subsequent rows of the first section (ndim2 > 0, and ndim3 == 0),
for the first element (ndim1 == 0), two elements from the prior row are
used:
current section:
* - - - - - - - - -
2 1 - - - - - - - -
- - - - - - - - - -
while for element after the first element, but before the last element
of the row, a full set of 4 elements is used:
current section:
- - - - 0 * - - - -
- - - - 3 2 1 - - -
- - - - - - - - - -
For the last element of a row (ndim1 == dim1-1), two elements are used
current section:
- - - - - - - - 0 *
- - - - - - - - - 2
- - - - - - - - - -
For sections after the first section, provided the
CBF_UNCORRELATED_SECTIONS flag is not set in the compression, for each
non-NULL entry in trail_char_data [0..3] an entry is made in
trail_char_data [4..7], except for the first element of the first row of
a section. In that case an entry is made in trail_char_data[4].
The structure of the compressed data is:
Byte Value
1 .. 8 Number of elements (64-bit little-endian number)
9 .. 16 Minumum element (currently unused)
17 .. 24 Maximum element (currently unused)
25 .. 32 (reserved for future use)
33 .. Coded data
3.3.3 Byte_offset compression
Starting with CBFlib 0.7.7, CBFlib supports a simple and efficient
"byte_offset" algorithm originally proposed by Andy Hammerley and
modified by Wolgang Kabsch and Herbert Bernstein. The original proposal
was called "byte_offsets". We distinguish this variant by calling it
"byte_offset". The major differences are that the "byte_offsets"
algorithm started with explicit storage of the first element of the
array as a 4-byte signed two's integer, and checked for image edges to
changes the selection of prior pixel. The CBFlib "byte_offset"
alogorithm starts with an assumed zero before the first pixel and
represents the value of the first pixel as an offset of whatever number
of size is needed to hold the value, and for speed, treats the entire
image as a simple linear array, allowing use of the last pixel of one
row as the base against which to compute the offset for the first
element of the next row.
The algorithm is simple and easily implemented. This algorithm can never
achieve better than a factor of two compression relative to 16-bit raw
data or 4 relative to 32-bit raw data, but for most diffraction data the
compression will indeed be very close to these ideal values. It also has
the advantage that integer values up to 32 bits (or 31 bits and sign)
may be stored efficiently without the need for special over-load tables.
It is a fixed algorithm which does not need to calculate any image
statistics, so is fast.
The algorithm works because of the following property of almost all
diffraction data and much other image data: The value of one element
tends to be close to the value of the adjacent elements, and the vast
majority of the differences use little of the full dynamic range.
However, noise in experimental data means that run-length encoding is
not useful (unless the image is separated into different bit-planes). If
a variable length code is used to store the differences, with the number
of bits used being inversely proportional to the probability of
occurrence, then compression ratios of 2.5 to 3.0 may be achieved.
However, the optimum encoding becomes dependent of the exact properties
of the image, and in particular on the noise. Here a lower compression
ratio is achieved, but the resulting algorithm is much simpler and more
robust.
The "byte_offset" compression algorithm is the following:
1. Start with a base pixel value of 0.
2. Compute the difference delta between the next pixel value and the
base pixel value.
3. If -127 =< delta =< 127, output delta as one byte, make the current
pixel value the base pixel value and return to step 2.
4. Otherwise output -128 (80 hex).
5. We still have to output delta. If -32767 =< delta =< 32767, output
delta as a little_endian 16-bit quantity, make the current pixel
value the base pixel value and return to step 2.
6. Otherwise output -32768 (8000 hex, little_endian, i.e. 00 then 80)
7. We still have to output delta. If -2147483647 =< delta =<
2147483647, output delta as a little_endian 32 bit quantity, make
the current pixel value the base pixel value and return to step 2.
8. Otherwise output -2147483648 (80000000 hex, little_endian, i.e. 00,
then 00, then 00, then 80) and then output the pixel value as a
little-endian 64 bit quantity, make the current pixel value the base
pixel value and return to step 2.
The "byte_offset" decompression algorithm is the following:
1. Start with a base pixel value of 0.
2. Read the next byte as delta
3. If -127 =< delta =< 127, add delta to the base pixel value, make
that the new base pixel value, place it on the output array and
return to step 2.
4. If delta is 80 hex, read the next two bytes as a little_endian
16-bit number and make that delta.
5. If -32767 =< delta =< 32767, add delta to the base pixel value, make
that the new base pixel value, place it on the output array and
return to step 2.
6. If delta is 8000 hex, read the next 4 bytes as a little_endian
32-bit number and make that delta
7. If -2147483647 =< delta =< 2147483647, add delta to the base pixel
value, make that the new base pixel value, place it on the output
array and return to step 2.
8. If delta is 80000000 hex, read the next 8 bytes as a little_endian
64-bit number and make that delta, add delta to the base pixel
value, make that the new base pixel value, place it on the output
array and return to step 2.
Let us look at an example, of two 1000 x 1000 flat field images
presented as a mimimal imgCIF file. The first image uses 32-bit unsigned
integers and the second image uses 16-bit unsigned integers.
The imgCIF file begins with some identifying comments (magic numbers) to
track the version of the dictionary and library:
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.7
This is followed by the necessary syntax to start a CIF data block and
by whatever tags and values are appropriate to describe the experiment.
The minimum is something like
data_testflat
eventually we come to the actual binary data, which begins the loop
header for the array_data category
loop_
_array_data.data
with any additional tags needed, and then the data itself, which starts
with the mini-header:
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 1000002
X-Binary-ID: 1
X-Binary-Element-Type: "unsigned 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: +FqUJGxXhvCijXMFHC0kaA==
X-Binary-Number-of-Elements: 1000000
X-Binary-Size-Fastest-Dimension: 1000
X-Binary-Size-Second-Dimension: 1000
X-Binary-Size-Padding: 4095
followed by an empty line and then the sequence of characters:
^L^Z^D<D5>
followed immediately by the compressed data.
The binary data begins with the hex byte 80 to flag the need for a value
that will not fit in one byte. That is followed by the small_endian hex
value 3E8 saying that the first delta is 1000. Then 999,999 bytes of
zero follow, since this is a flat field, with all values equal to zero.
That gives us our entire 1000x1000 compressed flat field. However,
because we asked for 4095 bytes of padding, there is an additional 4095
bytes of zero that are not part of the compressed field. They are just
pad and can be ignored. Finally, after the pad, the CIF text field that
began with
;
--CIF-BINARY-FORMAT-SECTION--
is completed with
--CIF-BINARY-FORMAT-SECTION----
;
notice the extra --
The second flat field then follows, with a very similar mini-header:
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 1000002
X-Binary-ID: 2
X-Binary-Element-Type: "unsigned 16-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: +FqUJGxXhvCijXMFHC0kaA==
X-Binary-Number-of-Elements: 1000000
X-Binary-Size-Fastest-Dimension: 1000
X-Binary-Size-Second-Dimension: 1000
X-Binary-Size-Padding: 4095
^L^Z^D<D5>
The only difference is that we have declared this array to be 16-bit and
have chosen a different binary id (2 instead of 1). Even the checksum is
the same.
4. Installation
CBFlib should be built on a disk with at least 200 megabytes of free
space. CBFlib.tar.gz is a "gzipped" tar of the code as it now stands.
Place the gzipped tar in the directory that is intended to contain a new
directory, named CBFlib_0.7.5 (the "top-level" directory) and uncompress
it with gunzip and unpack it with tar:
gunzip CBFlib.tar.gz
tar xvf CBFLIB.tar
As with prior releases, to run the test programs, you will also need
Paul Ellis's sample MAR345 image, example.mar2300, and Chris Nielsen's
sample ADSC Quantum 315 image, mb_LP_1_001.img as sample data. Both
these files will be extracted by the Makefile from
CBFlib_0.7.7_Data_Files. Do not download copies into the top level
directory.
After unpacking the archive, the top-level directory should contain a
makefile:
Makefile Makefile for unix
and the subdirectories:
src/ CBFLIB source files
include/ CBFLIB header files
m4/ CBFLIB m4 macro files (used to build .f90 files)
examples/ Example program source files
doc/ Documentation
lib/ Compiled CBFLIB library
bin/ Executable example programs
html_images/ JPEG images used in rendering the HTML files
For instructions on compiling and testing the library, go to the
top-level directory and type:
make
The CBFLIB source and header files are in the "src" and "include"
subdirectories. The FCBLIB source and m4 files are in the "src" and "m4"
subdirectories. The files are:
src/ include/ m4/ Description
cbf.c cbf.h CBFLIB API
functions
cbf_alloc.c cbf_alloc.h Memory allocation
functions
cbf_ascii.c cbf_ascii.h Function for
writing ASCII
values
cbf_binary.c cbf_binary.h Functions for
binary values
cbf_byte_offset.c cbf_byte_offset.h Byte-offset
compression
cbf_canonical.c cbf_canonical.h Canonical-code
compression
cbf_codes.c cbf_codes.h Encoding and
message digest
functions
cbf_compress.c cbf_compress.h General
compression
routines
cbf_context.c cbf_context.h Control of
temporary files
cbf_file.c cbf_file.h File in/out
functions
cbf_lex.c cbf_lex.h Lexical analyser
cbf_packed.c cbf_packed.h CCP4-style
packing compression
cbf_predictor.c cbf_predictor.h Predictor-Huffman
compression (not
implemented)
cbf_read_binary.c cbf_read_binary.h Read binary
headers
cbf_read_mime.c cbf_read_mime.h Read MIME-encoded
binary sections
cbf_simple.c cbf_simple.h Higher-level
CBFlib functions
cbf_string.c cbf_string.h Case-insensitive
string comparisons
cbf_stx.c cbf_stx.h Parser (generated
from cbf.stx.y)
cbf_tree.c cbf_tree.h CBF
tree-structure
functions
cbf_uncompressed.c cbf_uncompressed.h Uncompressed
binary sections
cbf_write.c cbf_write.h Functions for
writing
cbf_write_binary.c cbf_write_binary.h Write binary
sections
cbf.stx.y bison grammar to
define cbf_stx.c
(see WARNING)
md5c.c md5.h RSA message
digest software
from mpack
global.h
fcb_atol_wcnt.f90 Function to
convert a string to
an integer
fcb_ci_strncmparr.f90 Function to do a
case-insensitive
comparison of a
string to a byte
array
fcb_nblen_array.f90 Function to
determine the
non-blank length of
a byte array
fcb_read_byte.f90 Function to read
a single byte
fcb_read_line.f90 Function to read
a line into a byte
array
fcb_skip_whitespace.f90 Function to skip
whitespace and
comments in a MIME
header
fcb_exit_binary.m4 Function to skip
past the end of the
current binary text
field
fcb_next_binary.m4 Function to skip
to the next binary
fcb_open_cifin.m4 Function to open
a CBF file for
reading
fcb_packed.m4 Functions to read
a JPA CCP4
compressed image
fcb_read_bits.m4 Functions to read
nay number of bits
as an integer
fcb_read_image.m4 Functions to read
the next image in
I2, I4, 3D_I2 and
3D_I4 format
fcb_read_xds_i2.m4 Function to read
a single xds image.
fcblib_defines.m4 General m4 macro
file for FCBLIB
routines.
In the "examples" subdirectory, there are 2 additional files used by the
example programs (section 5) for reading MAR300, MAR345 or ADSC CCD
images:
img.c img.h Simple image library
and the example programs themselves:
makecbf.c Make a CBF file from an image
img2cif.c Make an imgCIF or CBF from an image
cif2cbf.c Copy a CIF/CBF to a CIF/CBF
convert_image.c Convert an image file to a cbf using a template file
cif2c.c Convert a template cbf file into a function to
produce the same template in an internal cbf data
structure
testcell.C Exercise the cell functions
as well as three template files: template_adscquantum4_2304x2304.cbf,
template_mar345_2300x2300.cbf, and
template_adscquantum315_3072x3072.cbf.
Two additional examples (test_fcb_read_image.f90 and
test_xds_binary.f90) are created from two files (test_fcb_read_image.m4
and test_xds_binary.m4) in the m4 directory.
The documentation files are in the "doc" subdirectory:
CBFlib.html This document (HTML)
CBFlib.txt This document (ASCII)
CBFlib_NOTICES.html Important NOTICES -- PLEASE READ
CBFlib_NOTICES.txt Important NOTICES -- PLEASE READ
gpl.txt GPL -- PLEASE READ
lgpl.txt LGPL -- PLEASE READ
cbf_definition_rev.txt Draft CBF/ImgCIF definition (ASCII)
cbf_definition_rev.html Draft CBF/ImgCIF definition (HTML)
cif_img.html CBF/ImgCIF extensions dictionary (HTML)
cif_img.dic CBF/ImgCIF extensions dictionary (ASCII)
ChangeLog,html Summary of change history (HTML)
ChangeLog Summary of change history (ASCII)
5. Example programs
The example programs makecbf.c, img2cif.c and convert_image.c read an
image file from a MAR300, MAR345 or ADSC CCD detector and then uses
CBFlib to convert it to CBF format (makecbf) or either imgCIF or CBF
format (img2cif). makecbf writes the CBF-format image to disk, reads it
in again, and then compares it to the original. img2cif just writes the
desired file. makecbf works only from stated files on disk, so that
random I/O can be used. img2cif includes code to process files from
stdin and to stdout. convert_image reads a template as well as the image
file and produces a complete CBF. The program convert_minicbf reads a
minimal CBF file with just and image and some lines of text specifying
the parameters of the data collection as done at SLS and combines the
result with a template to produce a full CBF. The program cif2cbf can be
used to convert among carious compression and encoding schemes. The
program sauter_test.C is a C++ test program contributed by Nick Sauter
to help in resolving a memory leak he found. The programs adscimg2cbf
and cbf2adscimg are a "jiffies" contributed by Chris Nielsen of ADSC to
convert ADSC images to imgCIF/CBF format and vice versa.
makecbf.c is a good example of how many of the CBFlib functions can be
used. To compile makecbf and the other example programs use the Makefile
in the top-level directory:
make all
This will place the programs in the bin directory.
makecbf
To run makecbf with the example image, type:
./bin/makecbf example.mar2300 test.cbf
The program img2cif has the following command line interface:
img2cif [-i input_image] \
[-o output_cif] \
[-c {p[acked]|c[annonical]|[n[one]}] \
[-m {h[eaders]|n[oheaders]}] \
[-d {d[igest]|n[odigest]}] \
[-e {b[ase64]|q[uoted-printable]| \
d[ecimal]|h[exadecimal]|o[ctal]|n[one]}] \
[-b {f[orward]|b[ackwards]}] \
[input_image] [output_cif]
the options are:
-i input_image (default: stdin)
the input_image file in MAR300, MAR345 or ADSC CCD detector
format is given. If no input_image file is specified or is
given as "-", an image is copied from stdin to a temporary file.
-o output_cif (default: stdout)
the output cif (if base64 or quoted-printable encoding is used)
or cbf (if no encoding is used). if no output_cif is specified
or is given as "-", the output is written to stdout
-c compression_scheme (packed, canonical or none, default packed)
-m [no]headers (default headers for cifs, noheaders for cbfs)
selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996)
headers within binary data value text fields.
-d [no]digest (default md5 digest [R. Rivest, RFC 1321, April
1992 using"RSA Data Security, Inc. MD5 Message-Digest
Algorithm"] when MIME headers are selected)
-e encoding (base64, quoted-printable, decimal, hexadecimal,
octal or none, default: base64) specifies one of the standard
MIME encodings (base64 or quoted-printable) or a non-standard
decimal, hexamdecimal or octal encoding for an ascii cif
or "none" for a binary cbf
-b direction (forward or backwards, default: backwards)
specifies the direction of mapping of bytes into words
for decimal, hexadecimal or octal output, marked by '>' for
forward or '<' for backwards as the second character of each
line of output, and in '#' comment lines.
cif2cbf
The test program cif2cbf uses many of the same command line options as
img2cif, but accepts either a CIF or a CBF as input instead of an image
file:
cif2cbf [-i input_cif] [-o output_cbf] \
[-u update_cif] \
[-c {p[acked]|c[annonical]|{b[yte_offset]}|\
{v[2packed}|{f[latpacked}[n[one]}] \
[-C highclipvalue] \
[-D ] \
[-I {0|2|4|8}] \
[-R {0|4|8}] \
[-L {0|4|8}] \
[-m {h[eaders]|noh[eaders]}] \
[-m {d[imensions]|nod[imensions}] \
[-d {d[igest]|n[odigest]|w[arndigest]}] \
[-B {read|liberal|noread}] [-B {write|nowrite}] \
[-S {read|noread}] [-S {write|nowrite}] \
[-T {read|noread}] [-T {write|nowrite}] \
[-e {b[ase64]|q[uoted-printable]|\
d[ecimal]|h[examdecimal|o[ctal]|n[one]}] \
[-b {f[orward]|b[ackwards]}\
[-p {1|2|4}\
[-v dictionary]* [-w] [-W]\
[input_cif] [output_cbf]
the options are:
-i input_cif (default: stdin)
the input file in CIF or CBF format. If input_cif is not
specified or is given as "-", it is copied from stdin to a
temporary file.
-o output_cbf (default: stdout)
the output cif (if base64 or quoted-printable encoding is used)
or cbf (if no encoding is used). if no output_cif is specified
or is given as "-", the output is written to stdout
if the output_cbf is /dev/null, no output is written.
-u update_cif (no default)
and optional second input file in CIF or CBF format containing
data blocks to be merged with data blocks from the primary
input CIF or CBF
The remaining options specify the characteristics of the
output cbf. Most of the characteristics of the input cif are
derived from context, except when modified by the -B, -S, -T, -v
and -w flags.
-b byte_order (forward or backwards, default forward (1234) on
little-endian machines, backwards (4321) on big-endian machines
-B [no]read or liberal (default noread)
read to enable reading of DDLm style brackets
liberal to accept whitespace for commas
-B [no]write (default write)
write to enable writing of DDLm style brackets
-c compression_scheme (packed, canonical, byte_offset,
v2packed, flatpacked or none,
default packed)
-C highclipvalue
specifies a double precision value to which to clip the data
-d [no]digest or warndigest (default md5 digest [R. Rivest,
RFC 1321, April 1992 using"RSA Data Security, Inc. MD5
Message-Digest Algorithm"] when MIME headers are selected)
-D test cbf_construct_detector
-e encoding (base64, k, quoted-printable or none, default base64)
specifies one of the standard MIME encodings for an ascii cif
or "none" for a binary cbf
-I 0 or integer element size
specifies integer conversion of the data, 0 to use the input
number of bytes, 2, 4 or 8 for short, long or long long
output integers
-L lowclipvalue
specifies a double precision value to cut off the data from
below
-m [no]headers (default headers)
selects MIME (N. Freed, N. Borenstein, RFC 2045, November 1996)
headers within binary data value text fields.
-m [nod]imensions (default dimensions)
selects detailed recovery of dimensions from the input CIF
for use in the MIME header of the output CIF
-p K_of_padding (0, 1, 2, 4) for no padding after binary data
1023, 2047 or 4095 bytes of padding after binary data
-R 0 or integer element size
specifies real conversion of the data, 0 to use the input
number of bytes, 4 or 8 for float or double output reals
-S [no]read or (default noread)
read to enable reading of whitespace and comments
-S [no]write (default write)
write to enable writing of whitespace and comments
-T [no]read or (default noread)
read to enable reading of DDLm style triple quotes
-T [no]write (default write)
write to enable writing of DDLm style triple quotes
-v dictionary specifies a dictionary to be used to validate
the input cif and to apply aliases to the output cif.
This option may be specified multiple times, with dictionaries
layered in the order given.
-w process wide (2048 character) lines
-W write wide (2048 character) lines
convert_image
The program convert_image requires two arguments: imagefile and cbffile.
Those are the primary input and output. The detector type is extracted
from the image file or from the command line, converted to lower case
and used to construct the name of a template cbf file to use for the
copy. The template file name is of the form template_name_columnsxrows.
The full set of options is:
convert_image [-i input_img] [-o output_cbf] [-p template_cbf]\
[-d detector name] -m [x|y|x=y] [-z distance] \
[-c category_alias=category_root]* \
[-t tag_alias=tag_root]* [-F] [-R] \
[input_img] [output_cbf]
the options are:
-i input_img (default: stdin)
the input file as an image in smv, mar300, or mar345 format.
If input_img is not specified or is given as "-", it is copied
from stdin to a temporary file.
-p template_cbf
the template for the final cbf to be produced. If template_cbf
is not specified the name is constructed from the first token
of the detector name and the image size as
template_<type>_<columns>x<rows>.cbf
-o output_cbf (default: stdout )
the output cbf combining the image and the template. If the
output_cbf is not specified or is given as "-", it is written
to stdout.
-d detectorname
a detector name to be used if none is provided in the image
header.
-F
when writing packed compression, treat the entire image as
one line with no averaging
-m [x|y|x=y] (default x=y, square arrays only)
mirror the array in the x-axis (y -> -y)
in the y-axis (x -> -x)
or in x=y ( x -> y, y-> x)
-r n
rotate the array n times 90 degrees counter clockwise
x -> y, y -> -x for each rotation, n = 1, 2 or 3
-R
if setting a beam center, set reference values of
axis settings as well as standard settings
-z distance
detector distance along Z-axis
-c category_alias=category_root
-t tag_alias=tagroot
map the given alias to the given root, so that instead
of outputting the alias, the root will be presented in the
output cbf instead. These options may be repeated as many
times as needed.
convert_minicbf
The program convert_minicbf requires two arguments: minicbf and cbffile.
Those are the primary input and output. The detector type is extracted
from the image file or from the command line, converted to lower case
and used to construct the name of a template cbf file to use for the
copy. The template file name is of the form template_name_columnsxrows.
The full set of options is:
convert_minicbf [-i input_cbf] [-o output_cbf] [-p template_cbf]\
[-q] [-C convention] \
[-d detector name] -m [x|y|x=y] [-z distance] \
[-c category_alias=category_root]* \
[-t tag_alias=tag_root]* [-F] [-R] \
[input_cbf] [output_cbf]
the options are:
-i input_cbf (default: stdin)
the input file as a CBF with at least an image.
-p template_cbf
the template for the final cbf to be produced. If template_cbf
is not specified the name is constructed from the first token
of the detector name and the image size as
template_<type>_<columns>x<rows>.cbf
-o output_cbf (default: stdout )
the output cbf combining the image and the template. If the
output_cbf is not specified or is given as "-", it is written
to stdout.
-q
exit quickly with just the miniheader expanded
after the data. No template is used.
-Q
exit quickly with just the miniheader unexpanded
before the data. No template is used.
-C convention
convert the comment form of miniheader into the
_array_data.header_convention convention
_array_data.header_contents
overriding any existing values
-d detectorname
a detector name to be used if none is provided in the image
header.
-F
when writing packed compression, treat the entire image as
one line with no averaging
-m [x|y|x=y] (default x=y, square arrays only)
mirror the array in the x-axis (y -> -y)
in the y-axis (x -> -x)
or in x=y ( x -> y, y-> x)
-r n
rotate the array n times 90 degrees counter clockwise
x -> y, y -> -x for each rotation, n = 1, 2 or 3
-R
if setting a beam center, set reference values of
axis settings as well as standard settings
-z distance
detector distance along Z-axis
-c category_alias=category_root
-t tag_alias=tagroot
map the given alias to the given root, so that instead
of outputting the alias, the root will be presented in the
output cbf instead. These options may be repeated as many
times as needed.
testreals, testflat and testflatpacked
The example programs testreals, testflat and testflatpacked exercise the
handling of reals, byte_offset compression and packed compression. Each
is run without any arguments. testreals will read real images from the
data file testrealin.cbf and write a file with real images in
testrealout.cbf, which should be identical to testrealin.cbf. testflat
and testflatpacked read 4 1000x1000 2D images and one 50x60x70 3D image
and produce an output file that should be identical to the input.
testflat reads testflatin.cbf and produces testflatout.cbf using
CBF_BYTE_OFFSET compression. testflatpacked reads testflatpackedin.cbf
and produces testflatpackedout.cbf. The images are:
* A 1000 x 1000 array of 32-bit integers forming a flat field with all
pixels set to 1000.
* A 1000 x 1000 array of 16-bit integers forming a flat field with all
pixels set to 1000.
* A 1000 x 1000 array of 32-bit integers forming a flat field with all
pixels set to 1000, except for -3 along the main diagonal and its
transpose.
* A 1000 x 1000 array of 16-bit integers forming a flat field with all
pixels set to 1000, except for -3 along the main diagonal and its
transpose.
* A 50 x 60 x 70 array of 32-bit integers in a flat field of 1000,
except for -3 along the main diagonal and the values i+j+k (counting
from zero) every 1000th pixel
test_fcb_read_image, test_xds_binary
The example programs test_fcb_read_image and test_xds_binary are
designed read the output of testflat and testflatpacked using the FCBlib
routines in lib/libfcb. test_xds_binary reads only the first image and
closes the file immediately. test_fcb_read_image reads all 5 images from
the input file. The name of the input file should be provided on stdin,
as in:
* echo testflatout.cbf | bin/test_xds_binary
* echo testflatpackedout.cbf | bin/test_xds_binary
* echo testflatout.cbf | bin/test_fcb_read_image
* echo testflatpackedout.cbf | bin/test_fcb_read_image
In order to compile these programs correctly for the G95 compiler it is
important to set the record size for reading to be no larger than the
padding after binary images. This in controlled in Makefile by the line
M4FLAGS = -Dfcb_bytes_in_rec=131072 which provides good performance for
gfortran. For g95, this line must be changed to M4FLAGS =
-Dfcb_bytes_in_rec=4096
sauter_test
The program sauter_test.C is a C++ test program contributed by Nick
Sauter to help in resolving a memory leak he found. The program is run
as bin/sauter_test and should run long enough to allow a check with top
to ensure that it has constant memory demands. In addition, starting
with release 0.7.8.1, the addition of -DCBFLIB_MEM_DEBUG to the compiler
flags will cause detailed reports on memory use to stderr to be
reported.
adscimg2cbf
The example program adscimg2cbf accepts any number of raw or compressed
ADSC images with .img, .img.gz, .img.bz2 or .img.Z extensions and
converts each of them to an imgCIF/CBF file with a .cbf extension.
adscimg2cbf [--flag[,modifier]] file1.img ... filen.img (creates file1.cbf ... filen.cbf)
Image files may also be compressed (.gz, .bz2, .Z)
Flags:
--cbf_byte_offset Use BYTE_OFFSET compression (DEFAULT)
--cbf_packed Use CCP4 packing (JPA) compression.
--cbf_packed_v2 Use CCP4 packing version 2 (JPA) compression.
--no_compression No compression.
The following two modifiers can be appended to the flags (syntax: --flag,modifier):
flat Flat (linear) images.
uncorrelated Uncorrelated sections.
adscimg2cbf
The example program cbf2adscimg accepts any number of cbfs of ADSC
images created by adscimg1cbf or convert_image and produces raw or
compressed adsc image files with .img, .img.gz or .img.bz2 extensions.
cbf2adscimg [--flag] file1.cbf ... filen.cbf (creates file1.img ... filen.img)
Image files may be compressed on output: (.gz, .bz2) by using the flags below.\n");
Flags:
--gz Output a .gz file (e.g., filen.img.gz).
--bz2 Output a .bz2 file (e.g., filen.img.bz2).
tiff2cbf
The test program tiff2cbf converts a tiff data file to a cbf data file.
The program converts the tiff data samples directly into a minicbf with
the tiff header stored at the value of _array_data.header_contents. This
conversion is supported for the sample formats SAMPLEFORMAT_UINT
(unsigned integer data), SAMPLEFORMAT_INT (unsigned integer data),
SAMPLEFORMAT_INT (signed integer data), SAMPLEFORMAT_IEEEFP (IEEE
floating point data), SAMPLEFORMAT_COMPLEXINT (complex signed int) and
SAMPLEFORMAT_COMPLEXIEEEFP (complex ieee floating). Conversions from
these formats to other CBF formats can be handled by cif2cbf. If you
wish to convert and xxx.tif written with IEEE floating point samples
into a CBF with integer values compressed by byte-offset compression for
use by XDS, creating an xxx_view.cbf with values clipped between 0 and
100, and an xxx_xds.cbf with unclipped values for processing:
tiff2cbf xxx.tif xxx.cbf
cif2cbf -I 4 -C 100. -L 0. -e n -c b -i xxx.cbf -o xxx_view.cbf
cif2cbf -I 4 -e n -c b -i xxx.cbf -o xxx_xds.cbf
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Updated 29 March 2011. Contact: yaya at bernstein-plus-sons dot com
