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CBFlib

An API for CBF/imgCIF
Crystallographic Binary Files with ASCII Support

Version 0.9.5
27 April 2014

by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory

and
Herbert J. Bernstein
Bernstein + Sons

© Copyright 2006, 2007, 2008, 2011, 2013, 2014 Herbert J. Bernstein


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.


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. Recent work on integration among CBF, HDF5 and NeXus supported in part by Pandata ODI (EU 7th Framework Programme)


Version History

Version DateByDescription
  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 HJB)   This release fixed a memory leak due 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, HJBIdentical 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, PC, GW, JH, HJB    Release with EZ's 2008 DDLm support using JH's PyCifRW, also cbff f95 wrapper code, PC's java bindings.
  0.9.1  Aug 2010  PC, EE, JLM, NS, EZ, HJB   Release with EE's Dectris template software, also with vcif3, new arvai_test, sequence_match.
  0.9.2   Feb 2011   PC, EE, JLM, NS, EZ, HJB   New default release with updated pycbf, tiff support, removal of default use of PyCifRW to avoid Fedora license issue.
  0.9.3   Oct 2013   JS, HJB   Added low-level 'cbf_H5*' functions for interacting with HDF5, higher level functions for converting CBF or miniCBF files to NeXus format, two utility programs to convert CBF or miniCBF files to NeXus format and some unit tests for the low-level 'cbf_H5*' functions. Add initial FEL detector support.
  0.9.4   March 2014   JS, HJB   Refactored implementation of the NXMX application defintion functional mapping with improvements to cmake support and a preliminary effort at handling Stokes polarization mapping. This release had serious issues in the functional mapping axis mapping and should not be used for production involving NeXus files.
  0.9.5   April 2014   HJB   This is a production release for single detector module single crystal MX NeXus support.


Known Problems

The example program tiff2cbf needs the enviroment variable LD_LIBRARY_PATH set to the location of the lib directory in CBFlib_0.9.2.11, 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 0.9.2.11 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:

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 450 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 :

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_0.9.2.11_Data_Files_Input. Do not download copies into the top level directory.

In addition, the kit will need tiff and hdf5 libraries.

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. For newer OS X systems, the default Makefile should work.

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:

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_0.9.5_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 0.9.5 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_0.9.2.11 directory. If a system copy is desired, download and install http://downloads.sf.net/cbflib/tiff-3.9.4-rev-6Feb11.tar.gz


Contents

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 CBF positioner handles

To represent an arbitrary positioning system designated by the terminal axis, CBFlib uses a value of type cbf_positioner.

A positioner object is created and initialized from a CBF object using one of the functions cbf_construct_positioner, cbf_construct_reference_positioner or cbf_require_reference_positioner.

The function cbf_free_positioner destroys a positioner handle and frees all memory associated with the corresponding object.

2.1.5 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:

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_NIBBLE_OFFSET  Simple "nibble_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 Å.

    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 Å to wavelength.

    ARGUMENTS
      handle  CBF handle.
      wavelength  Wavelength in Å.

    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
      handleCBF handle.
      reservedUnused. Any value other than 0 is invalid.
      timeTimestamp in seconds since January 1 1970.
      timezoneTimezone difference from UTC in minutes or CBF_NOTIMEZONE.
      precisionTimestamp 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 canŐt 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 canŐt 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_CANONICALCanonical-code compression (section 3.3.1)
    CBF_PACKEDCCP4-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_NIBBLE_OFFSET  Simple "nibble_offset" compression.
    CBF_NONENo 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_count_axis_ancestors, cbf_get_axis_ancestor, cbf_get_axis_depends_on,
    cbf_get_axis_equipment, cbf_get_axis_equipment_component,
    cbf_get_axis_offset,
    cbf_get_axis_rotation, cbf_get_axis_rotation_axis,
    cbf_get_axis_setting,
    cbf_get_axis_type,
    cbf_get_axis_vector

    PROTOTYPE

    #include "cbf_simple.h"

    int cbf_count_axis_ancestors (cbf_handle handle, const char *axis_id, unsigned int *ancestors);

    int cbf_get_axis_ancestor (cbf_handle handle, const char *axis_id, const unsigned int ancestor_index, const char * *ancestor);

    int cbf_get_axis_depends_on (cbf_handle handle, const char *axis_id, const char * *depends_on);

    int cbf_get_axis_equipment (cbf_handle handle, const char *axis_id, const char * *equipment);

    int cbf_get_axis_equipment_component (cbf_handle handle, const char *axis_id, const char * *equipment_component);

    int cbf_get_axis_offset (cbf_handle handle, const char *axis_id, double *offset1, double *offset2, double *offset3);

    int cbf_get_axis_rotation (cbf_handle handle, const char *axis_id, double *rotation);

    int cbf_get_axis_rotation_axis (cbf_handle handle, const char *axis_id, const char * *rotation_axis);

    int cbf_get_axis_setting (cbf_handle handle, unsigned int reserved, const char *axis_id, double *start, double *increment);

    int cbf_get_axis_type (cbf_handle handle, const char *axis_id, cbf_axis_type *axis_type);

    int cbf_get_axis_vector (cbf_handle handle, const char *axis_id, double *vector1, double *vector2, double *vector3);

    DESCRIPTION

    cbf_count_axis_ancestors sets ancestors to the number of ancestors of axis axis_id. cbf_get_axis_ancestor sets *ancestor to the ancestor axis of index ancestor_index of axis axis_id, starting with axis_id for ancestor_index 0.

    cbf_get_axis_depends_on sets *depends_on to the immediate ancestor of axis_id or to "." if there is no such ancestor. cbf_get_axis_equipment sets *equipment to the equipment of axis_id or to "." if there is no such equipment. cbf_get_axis_equipment_component sets *equipment_component to the equipment_component of axis_id or to "." if there is no such equipment_component.

    cbf_get_axis_offset sets *offset1, *offset2 and *offset3 to the components of the ofset of axis_id.

    cbf_get_axis_rotation sets rotation to the rotation of axis_id or to 0 if there is no such rotation. cbf_get_axis_rotation_axis sets *rotation_axis to the rotation_axis of axis_id or to "." if there is no such rotation_axis.

    cbf_get_axis_setting sets *start and *increment to the corresponding values of the axis axis_id. Any of the destination pointers may be NULL.

    cbf_get_axis_type sets axis_type to the type of axis_id.

    cbf_get_axis_vector sets *vector1, *vector2 and *vector3 to the components of the vector of axis_id.

    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.
      ancestor_index  Integer index of the desired ancestor, starting with 0 for the current axis_id.
      ancestor  Pointer to destination ancestor name pointer.
      depends_on  Pointer to destination depends_on name pointer.
      equipment  Pointer to destination equipment name pointer.
      equipment_component  Pointer to destination equipment_component name pointer.
      offset1  Pointer to destination first offset component value.
      offset2  Pointer to destination second offset component value.
      offset3  Pointer to destination third offset component value.
      rotation  Pointer to destination rotation value.
      rotation_axis  Pointer to destination rotation_axisn name pointer.
      start  Pointer to the destination start value.
      increment  Pointer to the destination increment value.
      type  Pointer to destination axis type of type .
      vector1  Pointer to destination first vector component value.
      vector2  Pointer to destination second vector component value.
      vector3  Pointer to destination third vector component 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 Å 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 Å.
      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_construct_positioner, cbf_construct_reference_positioner,

    PROTOTYPE

    #include "cbf_simple.h"

    int cbf_construct_positioner (cbf_handle handle, cbf_positioner *positioner, const char *axis_id);

    int cbf_construct_reference_positioner (cbf_handle handle, cbf_positioner *positioner, const char *axis_id);

    DESCRIPTION

    cbf_construct_positioner constructs a positioner object for the axis given by axis_id using the description in the CBF object handle and initialises the positioner handle *positioner.

    cbf_construct_reference positioner constructs a positioner object for the axis given by axis_id using the description in the CBF object handle and initialises the detector handle *detector using the reference settings of the axes.

    ARGUMENTS
      handle  CBF handle.
      detector  Pointer to the destination detector handle.
      axis_id  The identifier of the axis in the "axis" category.

    RETURN VALUE

    Returns an error code on failure or 0 for success.


    2.4.39 cbf_free_positioner

    PROTOTYPE

    #include "cbf_simple.h"

    int cbf_free_positioner (cbf_positioner positioner);

    DESCRIPTION

    cbf_free_positioner destroys the positioner object specified by positioner and frees all associated memory.

    ARGUMENTS
      positioner  Positioner handle to free.

    RETURN VALUE

    Returns an error code on failure or 0 for success.


    2.4.40 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.


    2.4.41 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.


    2.4.42 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.


    2.4.43 cbf_get_detector_axis_slow, cbf_get_detector_axis_slow, cbf_get_detector_axes, cbf_get_detector_axes_fs, cbf_get_detector_axes_sf, cbf_get_detector_surface_axes

    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);
    int cbf_get_detector_surface_axes(cbf_detector detector, const char * * axis_id1, const char * * axis_id2);

    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. cbf_get_detector_surface_axes sets *axis_id1 and *axis_id2 to the names of the two surface axes of the detector or ".",

    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.
      axis_id1  Pointer to the destination first surface axis name.
      axis_id1  Pointer to the destination first surface axis name.
      axis_id2  Pointer to the destination second surface axis name.

    RETURN VALUE

    Returns an error code on failure or 0 for success.


    2.4.44 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.


    2.4.45 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.


    2.4.46 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.


    2.4.47 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.


    2.4.48 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.


    2.4.49 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.


    2.4.50 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 Ångstroms, cell[3:5] to the double values of the cell angles α, β and γ 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 Ångstroms, cell_esd[3:5] to the double values of the estimated standard deviations of the the cell angles α, β and γ 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

    2.4.51 cbf_set_unit_cell
    2.4.52 cbf_get_reciprocal_cell
    2.4.53 cbf_set_reciprocal_cell
    2.4.54 cbf_compute_cell_volume
    2.4.55 cbf_compute_reciprocal_cell


    2.4.51 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 Ångstroms, the double values given in cell[3:5] for the cell angles α, β and γ 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 Ångstroms, and the double values given in cell_esd[3:5] for the estimated standard deviations of the the cell angles α, β and γ 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

    2.4.50 cbf_get_unit_cell
    2.4.52 cbf_get_reciprocal_cell
    2.4.53 cbf_set_reciprocal_cell
    2.4.54 cbf_compute_cell_volume
    2.4.55 cbf_compute_reciprocal_cell


    SEE ALSO

    2.4.52 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 Ångstroms-1, cell[3:5] to the double values of the reciprocal cell angles α*, β* and γ* 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 Ångstroms-1, cell_esd[3:5] to the double values of the estimated standard deviations of the the reciprocal cell angles α*, β* and γ* 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

    2.4.50 cbf_get_unit_cell
    2.4.51 cbf_set_unit_cell
    2.4.53 cbf_set_reciprocal_cell
    2.4.54 cbf_compute_cell_volume
    2.4.55 cbf_compute_reciprocal_cell


    2.4.53 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 Ångstroms-1, the double values given in cell[3:5] for the reciprocal cell angles α*, β* and γ* 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 Ångstroms, and the double values given in cell_esd[3:5] for the estimated standard deviations of the reciprocal cell angles α*, β* and γ* 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

    2.4.50 cbf_get_unit_cell
    2.4.51 cbf_set_unit_cell
    2.4.52 cbf_get_reciprocal_cell
    2.4.54 cbf_compute_cell_volume
    2.4.55 cbf_compute_reciprocal_cell


    2.4.54 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 Ångstroms and the double values given in cell[3:5] for the cell angles α, β and γ 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

    2.4.50 cbf_get_unit_cell
    2.4.51 cbf_set_unit_cell
    2.4.52 cbf_get_reciprocal_cell
    2.4.53 cbf_set_reciprocal_cell
    2.4.55 cbf_compute_reciprocal_cell


    2.4.55 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 Ångstroms, and the double values cell[3:5] giving the cell angles α, β and γ in degrees. The double values rcell[0:2] will be set to the reciprocal cell lengths a*, b* and c* in Ångstroms-1 and the double values rcell[3:5] will be set to the reciprocal cell angles α*, β* and γ* 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

    2.4.50 cbf_get_unit_cell
    2.4.51 cbf_set_unit_cell
    2.4.52 cbf_get_reciprocal_cell
    2.4.53 cbf_set_reciprocal_cell
    2.4.54 cbf_compute_cell_volume


    2.4.56 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.


    2.4.57 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.


    2.4.58 cbf_get_axis_poise, cbf_get_goniometer_poise, cbf_get_reference_poise

    PROTOTYPE

    #include "cbf_simple.h"

    int cbf_get_axis_poise(cbf_handle handle, double ratio, double * vector1, double * vector2, double * vector3, double * offset1, double * offset2, double * offset3, double * angle, const char * axis_id, const char * frame_id);
    int cbf_get_goniometer_poise(cbf_goniometer goniometer, double ratio, double * vector1, double * vector2, double * vector3, double * offset1, double * offset2, double * offset3, double * angle);
    int cbf_get_axis_reference_poise(cbf_handle handle, double * vector1, double * vector2, double * vector3, double * offset1, double * offset2, double * offset3, const char * axis_id);

    DESCRIPTION

    cbf_get_axis_poise sets vector1, vector2, vector3 to point to the components of the axis vector for axis axis_id, offset1, offset2, offset3 to point to the components of the axis base offset vector for axis axis_id, and angle to point to the angle of rotation of axis axis_id after application of the axis settings for frame frame_id, using ratio, a value between 0 and 1, indicating how far into the internal motion in the frame to go. If frame_id is the string ".", the first frame found is used. If there is more than one frame, which frame will be found is indeterminate. If frame_id is NULL, the overall setting for the scan are used, rather than those for any particular frame. The vector and offset reported are the reference vector and offset of the axis axis_id transformed by application of all motions of the axes on which axis_id depends.

    cbf_get_goniometer_poise vector1, vector2, vector3 to point to the components of the axis vector for the goniometer axis, offset1, offset2, offset3 to point to the components of the axis base offset vector for the goniometer axis, and angle to point to the angle of rotation of the goniometer axis after application of all axis settings in the goniometer deriving the vector, offset and angle from the resulting matrix. Calculation of the vector is indeterminate if the angle is zero.

    cbf_get_axis_reference_poise sets vector1, vector2, vector3 to point to the components of the axis vector for axis axis_id, offset1, offset2, offset3 to point to the components of the axis base offset vector for axis axis_id unmodified by axis rotations. Any of the pointers may be specified as NULL.

    ARGUMENTS
      handle  CBF handle.
      ratio  A number between 0 and 1 indication how far into the frame to go
      vector1  Pointer to the first component of the axis vector
      vector2  Pointer to the second component of the axis vector
      vector3  Pointer to the third component of the axis vector
      offset1  Pointer to the first component of the axis offset
      offset2  Pointer to the second component of the axis offset
      offset3  Pointer to the third component of the axis offset
      angle  Pointer to the rotation angle
      axis_id  The specified axis
      frame_id  The specified frame
      positioner  CBF goniometer

    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


    2.6 HDF5 abstraction layer and convenience functions

    The HDF5 abstraction layer mostly follows the HDF5 naming convention of H5Xfunction_name, where X is usually a single letter identifying the section of the API that the function resides in. A cbf_ prefix is used on all functions to avoid naming conflicts and make it clear that all these functions use the CBFlib error handling method whenever an error may occur.

    The main purpose of this API is to not to reimplement the HDF5 API, but to make common HDF5-related tasks easier when working with HDF5 files within CBFlib. The API therefore doesn't attempt to cover every possible use of HDF5, but to simplify common tasks. Use of the HDF5 API is not unexpected in library or user code, but functions in this section should be preferred in order to reduce development time and the amount of debugging required. A relatively comprehensive test program is provided, this should be used to verify that the functions in this section of the API are performing as expected and can be used as a source of example code.

    This section describes functions available for working with:

    Rank of a dataset

    Where a rank is required it must be equal to the length of the dim, max & chunk parameters, if they are given, and should be:

    • 0, for scalar data
    • 1, for vector data
    • 2, for matrix data
    • 3, for volume data
    • etc...

    The maximum rank is defined by the HDF5 library, a negative rank makes no sense and will often be treated as an error.

    HDF5-specific datatypes

    Any type parameters defining types for data stored in a file should usually be a value returned by cbf_H5Tcreate_string or one of the standard or IEEE types:

    H5T_STD_I8LE H5T_STD_I16LE H5T_STD_I32LE H5T_STD_I64LE
    H5T_STD_U8LE H5T_STD_U16LE H5T_STD_U32LE H5T_STD_U64LE
    H5T_STD_I8BE H5T_STD_I16BE H5T_STD_I32BE H5T_STD_I64BE
    H5T_STD_U8BE H5T_STD_U16BE H5T_STD_U32BE H5T_STD_U64BE
    H5T_IEEE_F32LE H5T_IEEE_F64LE H5T_IEEE_F32BE H5T_IEEE_F64BE

    Any type parameters defining types for data stored in memory should usually be a value returned by cbf_H5Tcreate_string or one of the native types:

    H5T_NATIVE_SCHAR H5T_NATIVE_SHORT H5T_NATIVE_INT H5T_NATIVE_LONG H5T_NATIVE_LLONG
    H5T_NATIVE_UCHAR H5T_NATIVE_USHORT H5T_NATIVE_UINT H5T_NATIVE_ULONG H5T_NATIVE_ULLONG
    H5T_NATIVE_FLOAT H5T_NATIVE_DOUBLE H5T_NATIVE_LDOUBLE

    Functions are rarely (if ever) limited to the above values, and can take any valid HDF5 datatype. The above is not a complete list of all available types, check the HDF5 documentation for such a list if you need one.

    Comparing data

    Some of the functions in this section will require a comparison function and some comparison parameters to be provided. The function should return zero if the data in the two arrays are considered equal and non-zero otherwise, note that this is the same as C's strcmp(). The signature of the comparison functions used here is:

    int compare (const void * expected, const void * existing, size_t length, const void * params)

    This will be called with:

    Type Name Description
    const void * expected A pointer to the array of requested values that was passed to the function.
    const void * existing An array of existing values read from the object.
    size_t length The length of the expected and existing arrays.
    const void * params A pointer to the comparison parameters which were passed to the calling function.

    The comparison parameters allow more complex comparisons to be performed, such as a check that the numbers are 'close enough' as determined by some variable measure of closeness. It is the caller's responsibility to ensure that the comparison function is appropriate for the type of data expected and that params is of the appropriate type for the comparison function. The parameters expected and existing should normally be cast to the appropriate type before being used.

    An example function for comparing ints, taken from the implementation of CBFlib:

    /*
    Compare two arrays of ints.
    Most parameters are defined as being 'const' even though
    the expected signature allows them to be mutable.
    */
    int cmp_int
        (const void * const expected,
         const void * const existing,
         size_t length,
         const void * const params)
    {
    	/*
        Cast the array pointers to the appropriate type, preserving the const-ness of the data.
        I won't be using any parameters for this comparison, so just ignore that argument.
    	*/
        const int * A = expected;
        const int * B = existing;
    
    	/*
        Iterate through the arrays comparing each element and decrementing a counter.
        If any are not equal the loop will exit early with length being non-zero.
    	*/
        while (length && *A++ == *B++) --length;
    
    	/*
        Return a value indicating whether the arrays are equal.
    	*/
        return length;
    }

    Some older functions use a simpler 3-argument comparison function, which doesn't have a parameter that can be used to pass some extra information to or retrieve information from the function.


    2.6.1 cbf_H5Acreate

    Create a new attribute.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Acreate (const hid_t location, hid_t *const attr, const char *const name, const hid_t type, const hid_t space)

    DESCRIPTION

    Creates a new attribute of the object location with name given by name, optionally returning it in the attr variable. An error will occur if a similarly named attribute already exists.

    ARGUMENTS

    location

    The hdf5 group/file in which to put the attribute.

    attr

    A pointer to a HDF5 object identifier that is set to the location of a valid object if the function succeeds, otherwise is left untouched.

    name

    The name of the existing/new dataset.

    type

    The type of data to be stored in the attribute.

    space

    The dataspace of the attribute.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.2 cbf_H5Afind

    Try to locate an existing attribute.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Afind (const hid_t location, hid_t *const attr, const char *const name, const hid_t type, const hid_t space)

    DESCRIPTION

    Checks for the existance of an attribute with the given name at location with a datatype of type and dataspace of space. Will return CBF_NOTFOUND if it cannot be found, or open it if it already exists.

    If type is not a datatype then no check of the attribute datatype will be done. If space is not a dataspace then no checks of the attribute dataspace wil be done.

    ARGUMENTS

    location

    The hdf5 group/file in which to put the attribute.

    attr

    A pointer to a HDF5 object identifier that is set to the location of a valid object if the function succeeds, otherwise is left untouched.

    name

    The name of the existing/new attribute.

    type

    The type of data stored in the attribute, or an invalid identifier if it should not be checked.

    space

    The dataspace of the attribute, or an invalid identifier if it should not be checked.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.3 cbf_H5Aread

    Read an entire attribute from a file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Aread (const hid_t attr, const hid_t type, void *const buf)

    DESCRIPTION

    Reads all of the data from attr into buf, which should have been allocated as the native type indicated by mem_type.

    ARGUMENTS

    attr

    A valid hdf5 handle for an attribute.

    type

    The type of data in memory.

    buf

    The location where the data is to be stored.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.4 cbf_H5Aread_string

    Read an entire string attribute from a file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Aread_string (const hid_t attr, const char **const val)

    DESCRIPTION

    Read a string attribute into memory, returning a pointer that must be free'd by the caller in val.

    ARGUMENTS

    attr

    The attribute to read from.

    val

    A pointer to a place the string may be stored.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.5 cbf_H5Awrite

    Write an entire attribute to a file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Awrite (const hid_t attr, const hid_t type, void *const buf)

    DESCRIPTION

    Writes all of the data from buf, which should contain data if the type indicated by mem_type, into attr.

    ARGUMENTS

    attr

    A valid hdf5 handle for an attribute.

    type

    The type of data in memory.

    buf

    The address of the data to be written.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.6 cbf_H5Arequire_cmp2

    Check for an attribute with the given space/type/value, or set one if it doesn't exist.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Arequire_cmp2 (const hid_t ID, const char *const name, const int rank, const hsize_t *const dim, const hid_t fileType, const hid_t memType, const void *const value, void *const buf, int(*cmp)(const void *, const void *, size_t))

    DESCRIPTION

    Checks the existance of an attribute of the given name, size, type and value. Equal value is determined by a custom comparison function which may use some extra data for more sophisticated tests. A new attribute with the given properties will be created if none currently exist, the function will fail if an incompatible attribute exists.

    ARGUMENTS

    ID

    The HDF5 object that the attribute will be applied to.

    name

    The name of the attribute.

    rank

    The number of dimensions of the attribute data, 0 for scalar data.

    dim

    The length of each dimension, not used for scalar data.

    fileType

    The HDF5 type of the attribute data in the file.

    memType

    The HDF5 type of the attribute data in memory.

    value

    The data to be written to the attribute.

    buf

    A buffer to be used when reading an existing attribute of the same size.

    cmp

    A comparison function to test if a previously set value is equal to the value I asked for.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.7 cbf_H5Arequire_cmp2_ULP

    Check for an attribute with the given space/type/value, or set one if it doesn't exist.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Arequire_cmp2_ULP (const hid_t ID, const char *const name, const int rank, const hsize_t *const dim, const hid_t fileType, const hid_t memType, const void *const value, void *const buf, int(*cmp)(const void *, const void *, size_t, const void *), const void *const cmp_params)

    DESCRIPTION

    Checks the existance of an attribute of the given name, size, type and value. Equal value is determined by a custom comparison function which may use some extra data for more sophisticated tests. A new attribute with the given properties will be created if none currently exist, the function will fail if an incompatible attribute exists.

    ARGUMENTS

    ID

    The HDF5 object that the attribute will be applied to.

    name

    The name of the attribute.

    rank

    The number of dimensions of the attribute data, 0 for scalar data.

    dim

    The length of each dimension, not used for scalar data.

    fileType

    The HDF5 type of the attribute data in the file.

    memType

    The HDF5 type of the attribute data in memory.

    value

    The data to be written to the attribute.

    buf

    A buffer to be used when reading an existing attribute of the same size.

    cmp

    A comparison function to test if a previously set value is equal to the value I asked for.

    cmp_params

    A pointer to a data structure which may be used by the comparison function.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.8 cbf_H5Arequire_string

    Check for a scalar string attribute with a given value, or set one if it doesn't exist.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Arequire_string (const hid_t location, const char *const name, const char *const value)

    DESCRIPTION

    Forwarding function that calls cbf_H5Arequire_cmp2_ULP with the appropriate arguments to compare two strings. The strcmp function is used for string comparison, with a small wrapper to verify array length:

    /** a possible implementation of a function to compare two strings for equality */
    static int cmp_string
        (const void * const a,
         const void * const b,
         const size_t N,
         const void * const params)
    {
    	/* first ensure the arrays have one element each */
        if (1 != N) return 1;
    	/* then forward to 'strcmp' for the actual comparison */
        else return strcmp(a,b);
    }

    ARGUMENTS

    location

    HDF5 object to which the string attribute should/will belong.

    name

    The name of the attribute.

    value

    The value which the attribute should/will have.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.9 cbf_H5Afree

    Close a HDF5 attribute.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Afree (const hid_t ID)

    DESCRIPTION

    Attempt to close an attribute, but don't modify the identifier that described it.

    ARGUMENTS

    ID

    The HDF5 attribute to be closed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.10 cbf_H5Dcreate

    Creates a new dataset in the given location.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Dcreate (const hid_t location, hid_t *const dataset, const char *const name, const int rank, const hsize_t *const dim, const hsize_t *const max, const hsize_t *const chunk, const hid_t type)

    DESCRIPTION

    The dataset parameter gives a location to store the dataset for use by the caller, for example to add an attribute to it. If non-zero the returned handle MUST be free'd by the caller with cbf_H5Dfree.

    The dimensions of the dataset to create are given in dim. The maximum extents of the dataset are given in max, which uses the values in dim as defaults if set to a null pointer. Each element of max must be at least as large as the corresponding element of dim. The dataset created will be a fixed-size dataset unless one of the elements of max is set to H5S_UNLIMITED.

    A chunk size must be given in the chunk argument if any element of max is set to H5S_UNLIMITED or is greater than the corresponding element of dim. If the dataset should not be chunked then a null pointer should be given.

    The dim, max and chunk arrays - if given - must each contain rank elements.

    This function will fail if a link with the same name already exists in location.

    ARGUMENTS

    location

    The hdf5 group/file in which to put the dataset.

    dataset

    An optional pointer to a location where the dataset handle should be stored.

    name

    The name of the new dataset.

    rank

    The rank of the data.

    dim

    The dimensions of the dataset to create. Unused if rank == 0.

    max

    The maximum size of each dimension. Unused if rank == 0.

    chunk

    The chunk size for the dataset.

    type

    The type of each data element in the file.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.11 cbf_H5Dfind2

    Look for a dataset with the given properties.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Dfind2 (const hid_t location, hid_t *const dataset, const char *const name, const int rank, const hsize_t *const max, hsize_t *const buf, const hid_t type)

    DESCRIPTION

    Returns CBF_NOTFOUND without modifying dataset if no dataset exists and fails without modifying dataset if one with different properties exists. A dataset will be 'found' if it has the same name and a maximum size which is at least as big as the size requested in max.

    A buffer of rank elements pointed to by buf may be used to store the array of maximum extents for a potentially matching dataset, in order to avoid the use of malloc & free for very small amounts of memory.

    Use as:

    /* Get the return code from the function call, */
    const int found = cbf_H5Dfind(location, &dataset, ...);
    /* and check what it was: */
    if (CBF_SUCCESS==found) {
    	/* A dataset already existed and I have a handle for it: */
        use_existing_dataset(dataset);
    } else if (CBF_NOTFOUND==found) {
    	/* No matching dataset existed, so I can create one: */
    	cbf_H5Dcreate(location, &dataset, ...);
        use_new_datset(dataset);
    } else {
    	/*
        The function call failed, do something with the error.
        In this case, store it for later use and print a message.
    	*/
        error |= found;
         cbf_debug_print(cbf_strerror(error));
    }
    /* clean up: */
    cbf_H5Dfree(dataset);

    ARGUMENTS

    location

    The hdf5 group/file in which to put the dataset.

    dataset

    A pointer to a HDF5 object identifier that is set to the location of a valid object if the function succeeds, otherwise is left in an undefined state.

    name

    The name of the existing/new dataset.

    rank

    The rank of the data, must be equal to the length of the max and buf arrays, if they are given.

    max

    The (optional) maximum size of each dimension, pointer or an array of length rank where 0 <= max[i] <= H5S_UNLIMITED for i = [0, rank), unused if rank == 0.

    buf

    An optional buffer with rank elements which may be used to store the current maximum dimensions of a potential match to avoid a malloc/free call.

    type

    The type of each data element in the file. If an invalid type is given a dataset of any type may be returned.

    RETURN VALUE

    CBF_SUCCESS if a matching dataset was found, CBF_NOTFOUND if nothing with the same name was found, some other error code otherwise.

    SEE ALSO


    2.6.12 cbf_H5Drequire

    Ensure that a dataset exists, returning a handle to an existing dataset or creating a new dataset if needed.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Drequire (const hid_t location, hid_t *const dataset, const char *const name, const int rank, const hsize_t *const max, const hsize_t *const chunk, hsize_t *const buf, const hid_t type)

    DESCRIPTION

    Ensure a dataset of the given rank exists and can hold at least as many elements as specified in max. If no dataset exists then one will be created with dimensions of [0, 0, ... 0]. cbf_H5Dfind and cbf_H5Dcreate are used in the implementation of this function.

    An existing dataset may be found using cbf_H5Dfind2(location, dataset, name, rank, max, buf, type). If no dataset can be found then a dataset will be created by setting each element of a buffer of length rank to zero and using cbf_H5Dcreate(location, dataset, name, rank, buffer, max, chunk, type). A buffer of rank elements may be provided to avoid using malloc to allocate memory for a small array whose size may already be known.

    The value pointed to by dataset should be a valid object identifier if the function exits successfully, and will be left in an undefined state otherwise.

    This is roughly equivalent to:

    const int error = cbf_H5Dfind2(location, dataset, name, rank, max, buf, type);
    if (CBF_NOTFOUND==error) {
    	int i;
    	for (i = 0; i != rank; ++i) buf[i] = 0;
    	return cbf_H5Dcreate(location, dataset, name, rank, buf, max, chunk, type);
    } else {
    	/* 'error' may be 'CBF_SUCCESS' or could indicate an error: */
    	return error;
    }

    but contains more sophisticated error handling code and allows for some parameters to be omitted.

    ARGUMENTS

    location

    The hdf5 group/file in which to put the dataset.

    dataset

    A pointer to a location to store the dataset.

    name

    The name of the existing/new dataset.

    rank

    The rank of the data.

    max

    The (optional) maximum size of each dimension.

    chunk

    The chunk size used if creating a new dataset.

    buf

    An optional buffer with rank elements.

    type

    The type of each data element in the file.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.13 cbf_H5Dinsert

    Add some data to a datset, expanding the dataset to the appropriate size if needed.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Dinsert (const hid_t dataset, const hsize_t *const offset, const hsize_t *const stride, const hsize_t *const count, hsize_t *const buf, const void *const value, const hid_t type)

    DESCRIPTION

    Insert a slice of data into dataset with the appropriate offset & stride, ensuring that no existing data is lost due to resizing the dataset but not checking that previous data isn't being overwritten.

    The offset, stride, count and buf arrays must each have rank elements. If stride is set to the null pointer then a default of [1, 1, 1, ..., 1] will be used. An optional buffer may be provided in buf to avoid using malloc to allocate a small amount of memory whose size may actually be known at compile time.

    The value array should contain count[0] * count[1] * ... * count[rank-1] === product(count) elements of data.

    ARGUMENTS

    dataset

    The dataset to write the data to.

    offset

    Where to start writing the data.

    stride

    The number of elements in the dataset to step for each element to be written.

    count

    The number of elements in each dimension to be written.

    buf

    An optional buffer to avoid using the heap for small amounts of memory.

    value

    The address of the data to be written.

    type

    The type of data in memory.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.14 cbf_H5Dset_extent

    Change the extent of a chunked dataset to the values in dim.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Dset_extent (const hid_t dataset, const hsize_t *const dim)

    DESCRIPTION

    Forwards to a HDF5 function to change the extent of dataset. The dim array must have the same number of elements as the rank of the dataset, but this can't be checked within this function.

    ARGUMENTS

    dataset

    A handle for the dataset whose extent is to be changed.

    dim

    The new extent of the dataset, if the function succeeds.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.15 cbf_H5Dwrite2

    Add some data to the specified position in the dataset, without checking what (if anything) was there before.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Dwrite2 (const hid_t dataset, const hsize_t *const offset, const hsize_t *const stride, const hsize_t *const count, const void *const value, const hid_t type)

    DESCRIPTION

    Assumes the dataset has the appropriate size to contain all the data and overwrites any existing data that may be there. The rank of the dataset is assumed to be known, and the size of the array parameters is not tested. When rank is zero - in the case of scalar datasets - the offset, stride and count parameters are meaningless and should be omitted by setting them to zero.

    ARGUMENTS

    dataset

    The dataset to write the data to.

    offset

    Where to start writing the data, as an array of rank numbers.

    stride

    The number of elements in the dataset to step for each element to be written, where null is equivalent to a stride of [1, 1, 1, ..., 1], as an array of rank numbers.

    count

    The number of elements in each dimension to be written, as an array of rank numbers.

    value

    The address of the data to be written.

    type

    The type of data in memory.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.16 cbf_H5Dread2

    Extract some existing data from a dataset at a known position with memtype.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Dread2 (const hid_t dataset, const hsize_t *const offset, const hsize_t *const stride, const hsize_t *const count, void *const value, const hid_t type)

    DESCRIPTION

    Read some data from a given location in the dataset to an existing location in memory. Does not check the length of the array parameters, which should all have rank elements or (in some cases) be null. When rank is zero - in the case of scalar datasets - the offset, stride and count parameters are meaningless and should be omitted by setting them to zero.

    ARGUMENTS

    dataset

    The dataset to read the data from.

    offset

    Where to start writing the data, as an array of rank numbers.

    stride

    The number of elements in the dataset to step for each element to be written, where null is equivalent to a stride of [1, 1, 1, ..., 1], as an array of rank numbers.

    count

    The number of elements in each dimension to be written, as an array of rank numbers.

    value

    The location where the data is to be stored.

    type

    The type of data in memory.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.17 cbf_H5Drequire_scalar_F64LE2

    Write a scalar 64-bit floating point number as a dataset with comparison.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Drequire_scalar_F64LE2 (const hid_t location, hid_t *const dataset, const char *const name, const double value, int(*cmp)(const void *, const void *, size_t))

    DESCRIPTION

    Convenience function using the HDF5 abstraction layer to avoid the need to consider array-related parameters for a scalar dataset.It ensures that a scalar 64-bit IEEE floating point dataset exists with the appropriate name and (for an existing dataset) the correct value as determined by the comparison function cmp.

    ARGUMENTS

    location

    The group containing the new dataset.

    dataset

    An optional pointer to a place to store the new dataset.

    name

    The name of the new dataset.

    value

    The value of the new dataset.

    cmp

    A comparison function to test if a previously set value is equal to the value I asked for.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.18 cbf_H5Drequire_scalar_F64LE2_ULP

    Write a scalar 64-bit floating point number as a dataset with a user-defined comparison.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Drequire_scalar_F64LE2_ULP (const hid_t location, hid_t *const dataset, const char *const name, const double value, int(*cmp)(const void *, const void *, size_t, const void *), const void *const cmp_params)

    DESCRIPTION

    Convenience function using the HDF5 abstraction layer to avoid the need to consider array-related parameters for a scalar dataset. It ensures that a scalar 64-bit IEEE floating point dataset exists with the appropriate name and (for an existing dataset) the correct value as determined by the user-supplied comparison function cmp.

    It is implemented using some of the other dataset functions:

    • cbf_H5Dfind2
    • cbf_H5Dcreate
    • cbf_H5Dread2
    • cbf_H5Dwrite2

    ARGUMENTS

    location

    The group containing the new dataset.

    dataset

    An optional pointer to a place to store the new dataset.

    name

    The name of the new dataset.

    value

    The value of the new dataset.

    cmp

    A comparison function to test if a previously set value is equal to the value I asked for.

    cmp_params

    Some extra data which may be required by the comparison function.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.19 cbf_H5Drequire_flstring

    Write a single fixed-length string as a dataset.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Drequire_flstring (const hid_t location, hid_t *const dataset, const char *const name, const char *const value)

    DESCRIPTION

    Convenience function using the HDF5 abstraction layer to avoid the need to consider array-related parameters for a scalar dataset and to automatically set the string type to the correct size.

    ARGUMENTS

    location

    The group containing the new dataset.

    dataset

    An optional pointer to a place to store the new dataset.

    name

    The name of the new dataset.

    value

    The value of the new dataset.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.20 cbf_H5Dfree

    Close a HDF5 dataset.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Dfree (const hid_t ID)

    DESCRIPTION

    Attempt to close a dataset, but don't modify the identifier that described it.

    ARGUMENTS

    ID

    The HDF5 dataset to be closed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.21 cbf_H5Fopen

    Attempt to open an HDF5 file by file name.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Fopen (hid_t *const file, const char *const name)

    DESCRIPTION

    Will try to open a file of the given name with suitable values for some of it's properties to make memory leaks less likely.

    Warning: this function will destroy any existing data in the file, do not pass the name of any file containing data you want to keep.

    ARGUMENTS

    file

    A pointer to an HDF5 ID where the newly opened file should be stored.

    name

    The name of the file to attempt to open.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.22 cbf_H5Fclose

    Close a HDF5 file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Fclose (const hid_t ID)

    DESCRIPTION

    Attempt to close a file, but don't modify the identifier that described it.

    ARGUMENTS

    ID

    The HDF5 file to be closed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.23 cbf_H5Gcreate

    Attempt to create a group.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Gcreate (const hid_t location, hid_t *const group, const char *const name)

    DESCRIPTION

    Helper function to attempt to create a HDF5 group identified by name and return an error code, to make error handling more consistant. This will fail if a link with the same name already exists in parent.

    ARGUMENTS

    location

    The group that will contain the newly created group.

    group

    A pointer to a HDF5 ID type where the group will be stored.

    name

    The name that the group will be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.24 cbf_H5Gfind

    Check if a group exists.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Gfind (const hid_t location, hid_t *const group, const char *const name)

    DESCRIPTION

    Checks for the existance of a group with the given name and parent. Will return CBF_NOTFOUND if it cannot be found, or open it if it already exists. An error code will be returned if something other than a group exists at the specified location.

    ARGUMENTS

    location

    The group to be searched.

    group

    A pointer to a HDF5 ID type where the group will be stored.

    name

    The path (ie, name) of the group to be found.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.25 cbf_H5Grequire

    Ensure a group exists.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Grequire (const hid_t location, hid_t *const group, const char *const name)

    DESCRIPTION

    Checks for the existance of a group with the given name and parent. Will create the group if it cannot be found, or open it if it already exists. It is an error if a matching group cannot be found or created. This uses cbf_H5Gcreate to create any new groups.

    ARGUMENTS

    location

    The group that will contain the newly created group.

    group

    A pointer to a HDF5 ID type where the group will be stored.

    name

    The name that the group will be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.26 cbf_H5Gfree

    Close a HDF5 group.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Gfree (const hid_t ID)

    DESCRIPTION

    Attempt to close a group, but don't modify the identifier that described it.

    ARGUMENTS

    ID

    The HDF5 group to be closed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.27 cbf_H5Ivalid

    Check the validity of an object identifier.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Ivalid (const hid_t ID)

    DESCRIPTION

    Function to check validity of a HDF5 identifier. HDF5's predefined types are never counted as valid by this function, so it can't be used to test the validity of a type constant. Types obtained by using H5Tcopy are safe to test.

    ARGUMENTS

    ID

    An HDF5 object identifier.

    RETURN VALUE

    Non-zero if the type is valid, zero otherwise.

    SEE ALSO


    2.6.28 cbf_H5Ocmp

    A missing HDF5 function.

    PROTOTYPE

    #include "cbf_hdf5.h"
    htri_t cbf_H5Ocmp (const hid_t id0, const hid_t id1)

    DESCRIPTION

    Compare two HDF5 object ID's for equality. This follows the standard practice of returning zero if objects should be considered equal, and the HDF5 practice of returning a negative number if there is an error.

    ARGUMENTS

    id0

    An HDF5 identifier.

    id1

    An HDF5 identifier.

    RETURN VALUE

    0 if equal, a positive value if not equal, or a negative value if there is an error.

    SEE ALSO


    2.6.29 cbf_H5Ofree

    Close a HDF5 object identifier.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Ofree (const hid_t ID)

    DESCRIPTION

    Attempt to close an object identifier of unknown type, but don't modify the identifier that described it.

    ARGUMENTS

    ID

    The HDF5 object to be closed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.30 cbf_H5Screate

    Create a dataspace with some given values.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Screate (hid_t *const ID, const int rank, const hsize_t *const dim, const hsize_t *const max)

    DESCRIPTION

    Helper function which creates a HDF5 dataspace.

    Maximum dimensions can be set to infinity by passing H5S_UNLIMITED in the appropriate slot of the max parameter. If rank is zero then neither dim nor max are used and a scalar dataspace is created. If rank is non-zero and dim is a null pointer then ID will not be modified and the function will fail. If rank is non-zero and max is a null pointer the maximum length is set to the current length as given by dim.

    ARGUMENTS

    ID

    A pointer to a HDF5 identifier that will contain the new dataspace.

    rank

    The number of dimensions of the new dataspace.

    dim

    The current size of each dimension of the dataspace, should be an array of length rank .

    max

    The maximum size of each dimension, should be an array of length rank .

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.31 cbf_H5Sfree

    Close a HDF5 dataspace identifier.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Sfree (const hid_t ID)

    DESCRIPTION

    Attempt to close a dataspace identifier, but don't modify the identifier that described it.

    ARGUMENTS

    ID

    The HDF5 dataspace to be closed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.32 cbf_H5Tcreate_string

    Get a HDF5 string datatype to describe a sting of the specified length.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Tcreate_string (hid_t *const type, const size_t len)

    DESCRIPTION

    Convenience function to create a string datatype suitable for use when storing a string of length len, returning it in the identifier pointed to by type.

    ARGUMENTS

    type

    A pointer to a the HDF5 handle of the new datatype, which should be free'd with cbf_H5Tfree

    len

    The length of the string datatype - should be strlen() or H5T_VARIABLE

    RETURN VALUE

    An error code.

    SEE ALSO


    2.6.33 cbf_H5Tfree

    Close a HDF5 datatype identifier.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_H5Tfree (const hid_t ID)

    DESCRIPTION

    Attempt to close a datatype identifier, but don't modify the identifier that described it.

    ARGUMENTS

    ID

    The HDF5 datatype to be closed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7 High-level NeXus-related functions

    These functions primarily allow interaction with a cbf_h5handle without being exposed to its structure or the complexities of using it correctly. Wherever possible these functions should be used instead of directly accessing a cbf_h5handle or cbf_config_t in order make code easier to read, to maintain the integrity of the data structures and to ensure all resources allocated to these object are correctly cleaned up.

    This section describes functions available for working with:

    Reading miniCBF configuration settings

    This example demonstrates how a miniCBF configuration file should be parsed, what should be checked before the extracted settings are used and what should be cleaned up by the caller afterwards:

    /* Declare some important variables */
    int configError = cbf_configError_success;
    FILE * configFile = fopen("config.txt","r");
    cbf_config_t * const configSettings = cbf_config_create();
    
    /*
    Read and check the configuration settings,
    writing any error messages to stderr.
    */
    configError = cbf_config_parse(configFile,stderr,configSettings);
    /* I no longer need to keep the file open */
    fclose(configFile);
    
    /* Check if I could read the file successfully */
    if (cbf_configError_success != configError) {
        fprintf(stderr,"Error parsing configuration file 'config.txt': %s\n",
                cbf_config_strerror(configError));
    } else {
    	/* Use the configuration settings here... */
    }
    
    /* Clean up the settings to avoid memory leaks */
    cbf_config_free(configSettings);

    2.7.1 cbf_h5handle_get_file

    Get the current id of the file within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_file (const cbf_h5handle nx, hid_t *const file)

    DESCRIPTION

    Check the handle for the presence of a file, optionally returning it.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    file

    A place to store the file (if found), or null if the file isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.2 cbf_h5handle_set_file

    Set the id of the file within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_file (const cbf_h5handle nx, const hid_t file)

    DESCRIPTION

    Sets the file id within the handle to the given value. Doesn't check or modify any attributes in any way.

    ARGUMENTS

    nx

    The handle to add information to.

    file

    The file to be set as the current file id.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.3 cbf_h5handle_get_entry

    Get the current id and name of the entry group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_entry (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of an entry group and its name, optionally returning any combination of them. The error code 'CBF_NOTFOUND' will be returned if any of the requested items of data cannot be found.

    The handle retains ownership of the returned object and/or string, neither of them should be free'd by the caller.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.4 cbf_h5handle_set_entry

    Set the id and name of the entry group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_entry (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the entry group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current entry group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.5 cbf_h5handle_require_entry

    Ensure I have an entry in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_entry (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the entry group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "entry".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.6 cbf_h5handle_require_entry_definition

    Ensure I have an entry in the hdf5 handle with definition.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_entry_definition (const cbf_h5handle nx, hid_t *const group, const char *name, const char *definition, const char *version, const char *URL)

    DESCRIPTION

    This will check if the entry group and definition within the handle matches any existing group of the same name within the current file and has a definition designation that agrees. If the group name doesn't match a new group is opened or created and added to the handle. If the definition does not match, it is replaced with the new one. If the version attribute does not match it is replaced with the new one. If the URL> attribute does not match it is replace with the new one. The NX_class attributes are not checked, but if a new entry is created it will be created with NX_class NXentry.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group ID should be stored.

    name

    The group name, or null to use the default name of "entry".

    definition

    The definition name, or null to not specify a definition name.

    version

    The version string, or null to not specify a version string.

    URL

    The URL at which the definition is stored, or null to not specify a URL

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.7 cbf_h5handle_get_sample

    Get the current id and name of the sample group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_sample (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of an sample group and its name, optionally returning any combination of them.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.8 cbf_h5handle_set_sample

    Set the id and name of the sample group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_sample (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the sample group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current sample group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.9 cbf_h5handle_require_sample

    Ensure I have a sample in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_sample (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the sample group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "sample".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.10 cbf_h5handle_get_beam

    Get the current id and name of the beam group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_beam (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of a beam group and its name, optionally returning any combination of them. The error code 'CBF_NOTFOUND' will be returned if any of the requested items of data cannot be found.

    The handle retains ownership of the returned object and/or string, neither of them should be free'd by the caller.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.11 cbf_h5handle_set_beam

    Set the id and name of the beam group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_beam (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the beam group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current beam group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.12 cbf_h5handle_require_beam

    Ensure I have a beam in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_beam (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the beam group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "beam".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.13 cbf_h5handle_get_instrument

    Get the current id and name of the instrument group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_instrument (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of an instrument group and its name, optionally returning any combination of them. The error code 'CBF_NOTFOUND' will be returned if any of the requested items of data cannot be found.

    The handle retains ownership of the returned object and/or string, neither of them should be free'd by the caller.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.14 cbf_h5handle_set_instrument

    Set the id and name of the instrument group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_instrument (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the instrument group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current instrument group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.15 cbf_h5handle_find_instrument

    Find an existing instrument group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_find_instrument (const cbf_h5handle nx, hid_t *const group, const char **const name)

    ARGUMENTS

    nx
    group
    name

    2.7.16 cbf_h5handle_require_instrument

    Ensure I have an instrument in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_instrument (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the instrument group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "instrument".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.17 cbf_h5handle_get_detector

    Get the current id and name of the detector group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_detector (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of an detector group and its name, optionally returning any combination of them. The error code 'CBF_NOTFOUND' will be returned if any of the requested items of data cannot be found.

    The handle retains ownership of the returned object and/or string, neither of them should be free'd by the caller.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.18 cbf_h5handle_set_detector

    Set the id and name of the detector group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_detector (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the detector group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current detector group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.19 cbf_h5handle_find_detector

    Find an existing detector group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_find_detector (const cbf_h5handle nx, hid_t *const group, const char **const name)

    ARGUMENTS

    nx
    group
    name

    2.7.20 cbf_h5handle_require_detector

    Ensure I have a detector in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_detector (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the detector group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "detector".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.21 cbf_h5handle_get_goniometer

    Get the current id and name of the goniometer group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_goniometer (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of an goniometer group and its name, optionally returning any combination of them. The error code 'CBF_NOTFOUND' will be returned if any of the requested items of data cannot be found.

    The handle retains ownership of the returned object and/or string, neither of them should be free'd by the caller.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.22 cbf_h5handle_set_goniometer

    Set the id and name of the goniometer group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_goniometer (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the goniometer group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current goniometer group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.23 cbf_h5handle_require_goniometer

    Ensure I have a goniometer in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_goniometer (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the goniometer group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "goniometer".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.24 cbf_h5handle_get_monochromator

    Get the current id and name of the monochromator group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_monochromator (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of an monochromator group and its name, optionally returning any combination of them. The error code 'CBF_NOTFOUND' will be returned if any of the requested items of data cannot be found.

    The handle retains ownership of the returned object and/or string, neither of them should be free'd by the caller.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.25 cbf_h5handle_set_monochromator

    Set the id and name of the monochromator group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_monochromator (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the monochromator group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current monochromator group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.26 cbf_h5handle_require_monochromator

    Ensure I have a monochromator in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_monochromator (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the monochromator group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "monochromator".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.27 cbf_h5handle_get_source

    Get the current id and name of the source group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_get_source (const cbf_h5handle nx, hid_t *const group, const char **const name)

    DESCRIPTION

    Check the handle for the presence of an source group and its name, optionally returning any combination of them. The error code 'CBF_NOTFOUND' will be returned if any of the requested items of data cannot be found.

    The handle retains ownership of the returned object and/or string, neither of them should be free'd by the caller.

    ARGUMENTS

    nx

    A handle to query for the presence of the requested information.

    group

    A place to store the group (if found), or null if the group isn't wanted.

    name

    A place to store the name of the group (if found), or null if the name isn't wanted.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.28 cbf_h5handle_set_source

    Set the id and name of the source group within the given handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_set_source (const cbf_h5handle nx, const hid_t group, const char *const name)

    DESCRIPTION

    Sets the source group and name within the handle to the given values. Doesn't check or modify the NX_class attribute in any way. The handle will take ownership of the group id iff this function succeeds.

    ARGUMENTS

    nx

    The handle to add information to.

    group

    The group to be set as the current source group

    name

    The name which the group should be given.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.29 cbf_h5handle_require_source

    Ensure I have a source in the hdf5 handle.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_h5handle_require_source (const cbf_h5handle nx, hid_t *const group, const char *name)

    DESCRIPTION

    This will check if the source group within the handle matches any existing group of the same name within the current file. If they don't match a new group is opened or created and added to the handle. The NX_class attributes are not checked.

    ARGUMENTS

    nx

    The HDF5 handle to use.

    group

    An optional pointer to a place where the group should be stored.

    name

    The group name, or null to use the default name of "source".

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.30 cbf_free_h5handle

    Free a handle for an HDF5 file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_free_h5handle (cbf_h5handle h5handle)

    DESCRIPTION

    Checks if the handle appears to be valid, the free's the handle and any data that the handle owns.

    ARGUMENTS

    h5handle

    The handle to be free'd.

    RETURN VALUE

    An error code

    SEE ALSO


    2.7.31 cbf_create_h5handle3

    Allocates space for a HDF5 file handle and associates it with the given file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_create_h5handle3 (cbf_h5handle *handle, hid_t file)

    DESCRIPTION

    This function expects the user to create or open a hdf5 file with the appropriate parameters for what they are trying to do, replacing older functions which would create a file with the H5F_ACC_TRUNC flag and H5F_CLOSE_STRONG property.

    ARGUMENTS

    handle

    A pointer to a handle which is to be allocated.

    file

    A HDF5 file to store within the newly created handle.

    RETURN VALUE

    An error code

    SEE ALSO


    2.7.32 cbf_write_cbf_h5file

    Extract the data from a CBF file & put it into a NeXus file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_write_cbf_h5file (cbf_handle handle, cbf_h5handle h5handle)

    DESCRIPTION

    Equivalent to cbf_write_cbf2nx(handle,h5handle,0,0,0).

    ARGUMENTS

    handle

    The CBF file to extract data from.

    h5handle

    The NeXuS file to write data to.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.33 cbf_write_cbf2nx

    Extract the data from a CBF file & put it into a NeXus file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_write_cbf2nx (cbf_handle handle, cbf_h5handle h5handle, const char *const datablock, const char *const scan, const int list)

    DESCRIPTION

    Extracts data from handle and generates a NeXus file in h5handle. This will attempt to extract metadata and image data from each scan (or the named scan) within each datablock (or the the named datablock) and insert it into a given index into the NXentry group specified in h5handle.

    Each scan in the CBF file corresponds to one NXentry in NeXus, so a CBF datablock with multiple scans must be converted by calling this function with the appropriate value of scan once for each scan in the datablock.

    The flags (within h5handle) determine:

    • Compression algorithm: zlib/CBF/none
    • Plugin registration method: automatic/manual

    The strings given by h5handle->scan_id and h5handle->sample_id define:

    • The presence and value of an identifier for the scan, stored in /*:NXentry/entry_identifier.
    • The presence and value of an identifier for the sample, stored in /*:NXentry/*:NXsample/sample_identifier.

    ARGUMENTS

    handle

    The CBF file to extract data from.

    h5handle

    The NeXuS file to write data to.

    datablock

    The name of the datablock to convert, or NULL to convert all datablocks.

    scan

    The name of the scan to convert, or NULL if there is only one scan in the datablock.

    list

    Boolean flag to determine if a list of processed items is printed.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.34 cbf_write_minicbf_h5file

    Extract the data from a miniCBF file & put it into a NeXus file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_write_minicbf_h5file (cbf_handle handle, cbf_h5handle h5handle, const cbf_config_t *const axisConfig)

    DESCRIPTION

    Extracts the miniCBF data directly - by parsing the header - and uses that plus the configuration options from axisConfig to generate a NeXus file in h5handle. This can extract metadata and image data from miniCBF files containing multiple datablocks which each contain a single image and insert it into a given index into the NXentry group specified in h5handle.

    Currently, only Pilatus 1.2 format headers are supported.

    The flags determine:

    • Compression algorithm: zlib/CBF/none
    • Plugin registration method: automatic/manual

    ARGUMENTS

    handle

    The miniCBF file to extract data from.

    h5handle

    The NeXus file to write data to.

    axisConfig

    The configuration settings desribing the axes and their relation to the sample and to each other.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.35 cbf_write_nx2cbf

    Extract data from a nexus file and store it in a CBF file.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_write_nx2cbf (cbf_h5handle nx, cbf_handle cbf)

    DESCRIPTION

    Reads NeXus-format data from the entry group defined in the nx handle, extracting data related to the frame with index nx->slice and in CBF-format within the the cbf handle.

    ARGUMENTS

    nx

    The handle defining the NeXus data to be converted.

    cbf

    The handle in which to store the resulting CBF data.

    RETURN VALUE

    An error code.

    SEE ALSO


    2.7.36 cbf_config_create

    Obtain a new handle for some configuration settings.

    PROTOTYPE

    #include "cbf_hdf5.h"
    cbf_config_t* cbf_config_create ()

    DESCRIPTION

    Allocates a new collection of configuration settings on the heap, and initialises it. The returned pointer should be destroyed by the caller.

    ARGUMENTS

    This function takes no arguments.

    RETURN VALUE

    A newly allocated object for miniCBF configuration settings, or NULL.


    2.7.37 cbf_config_parse

    Read a minicbf configuration file into the given handle, writing errors to logfile.

    PROTOTYPE

    #include "cbf_hdf5.h"
    int cbf_config_parse (FILE *const configFile, FILE *const logFile, cbf_config_t *const vec)

    DESCRIPTION

    Parses a configuration file to extract a collection of configuration settings for a miniCBF file, storing them in the given configuration settings object. The pointer should have been obtained by a call to cbf_config_create. The configuration file format is described in the minicbf2nexus documentation.

    ARGUMENTS

    configFile

    The file from which the config settings should be read.

    logFile

    A stream to be used for logging error messages.

    vec

    An object describing the configuration settings.

    RETURN VALUE

    A parser error code.


    2.7.38 cbf_config_free

    Free any heap memory associated with the given cbf_hdf5_configItemVectorhandle object.

    PROTOTYPE

    #include "cbf_hdf5.h"
    void cbf_config_free (const cbf_config_t *const vector)

    DESCRIPTION

    Destroys an existing collection of configuration settings. The settings should have been obtained by a call to cbf_config_create.

    ARGUMENTS

    vector

    The configuration data to be free'd.

    RETURN VALUE

    Nothing.


    2.7.39 cbf_config_strerror

    Convert a parse error to a descriptive string.

    PROTOTYPE

    #include "cbf_hdf5.h"
    const char* cbf_config_strerror (const int error)

    DESCRIPTION

    The returned string is "none" for success, "unknown error" if the given error code is not recognised and a non-empty string briefly describing the error otherwise.

    The returned string must not be free'd.

    ARGUMENTS

    error

    An error returned by a cbf_config_* function.

    RETURN VALUE

    A string describing the error.


    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:

    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_PACKED_V2   0x0090 (144)
      CBF_BYTE_OFFSET   0x0070 (112)
      CBF_NIBBLE_OFFSET   0x00A0 (160)
      CBF_PREDICTOR   0x0080 (128)
      ...    

    The binary data then follows in bytes 29 through 29+n-1.

    The binary characters serve specific purposes:

    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:

    ByteASCII
    symbol
    Decimal 
    value
    Description
      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. 3. A simple and efficient byte-offset compression. 4. A slightly more complex nibble-offset compression.

    All encode the difference (or error) between the current element in the array and the prior element or neighboring elements.

    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:

    ByteValue
      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
    bits 3 .. 5
    Number of bits
    in each V1 offset

    Number of bits
    in each V2 offset

    000
    143
    254
    365
    476
    587
    6168
    7max9
    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:

    ByteValue
      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.

    3.3.4 Nibble_offset compression

    The nibble offset algorithm is a variant on A. P. Hammersley's byte offset algorithm. The major differences are that the compression modes are "sticky", the compression can be reset at any point to allow for block parallelism, and the basic unit of compression is the nibble, but for very clean data, the dibit is also supported.

    The data stream starts with and in general uses a mode-setting octet presented in one if three forms, a single dibit a0, two dibits a0, a1, or two dibits and a nibble a0, a1, b:

    a0 a1 b octet meaning
    00 00 0000 0x00 reset to zero
    01 0x01 up 1 mode
    10 0x02 dibit mode
    11 0x03 up n modes
    00 01 0x04 nibble mode
    00 11 0x0C 6-bit mode
    00 10 0x08 byte mode
    00 00 0011 0x30 12-bit word mode
    00 00 0001 0x10 16-bit word mode
    00 00 0010 0x20 32-bit word mode
    00 00 0100 0x40 64-bit word mode
    00 00 1100 0xC0 specify starting address

    The reset to zero is followed by a new mode octet A reset to zero resets the prior value for delta to zero

    The up n modes code is followed immediately by a dibit specifying 2 less than the number of modes by which to change, and then by a delta in the mode.

    Note that up n modes has no effect until an actual mode has been set and can be used immediately after a reset to pad to nibble, octet or double-word boundaries.

    Once a mode is established, it is followed by a stream of deltas of that size (for modes 2 or 4-64) or by one delta of that size and then a stream of deltas of the size that was in effect before an up or down giving little-endian offsets from the currently accumulated value. If the offset is one of the following in the indicated mode

    dibit mode 0x2
    nibble mode 0x8
    6-bit mode 0x20
    byte mode 0x80
    12-bit word mode 0x800
    16-bit word mode 0x8000
    32-bit word mode 0x8000 0000
    64-bit word mode 0x8000 0000 0000 0000

    it is followed by the new mode as 1 or 2 dibits or 2 dibits and a nibble a1 a1 b. If a1 is 1 or 2 or 3, that is the new mode. If a1 is zero and a2 is 1 or 2 the new mode is a2*4. If a2 is 3 the new mode is a2*2. If both a1 and a2 are zero, the new mode is b*16 unless b is 3. If b is 3 the new mode is b*4

    The 0xC0 flag is followed by a second mode giving the number of bytes of image starting offset address followed by the image offset address followed by the mode of that data. 0xC0 also acts as a reset. Use of the 0xC0 flag is not required. Addresses default to sequential starting from 0, but is provided to faciliate parallel compression.

    3.4 Access to CBFlib compressions from HDF5

    Starting with CBFlib release 0.9.2.11, a plugin module in provided to allow access to CBFlib compressions from HDF5 1.8.11 and later. For general documentation on HDF5 dynamically loaded filters, see http://www.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/HDF5DynamicallyLoadedFilters.pdf The discussion here will be confined to use of the CBFlib compressions plugin.

    The filter has been registered with the HDF5 group as 32006, and cbf.h includes the symbolic name for the filter CBF_H5Z_FILTER_CBF.

    The source and header of the CBFlib filter plugin are cbf_hdf5_filter.c and cbf_hdf5_filter.h. To use the filter in C applications, you will need to include cbf_hdf5_filter.h in the application and have the cbflib.so library in the search path used by HDF5 1.8.11. The HDF group says

    The default directory for an HDF5 filter plugin library is defined on UNIX- like systems as quot;/usr/local/hdf5/lib/plugin"
    and on Windows systems as "%ALLUSERSPROFILE%/hdf5/lib/plugin". The default path can be overwritten by a user with the HDF5_PLUGIN_PATH environment variable. Several directories can be specified for the search path using ":" as a path separator for UNIX-like systems and ";" for Windows.

    In the Makefile, tests are done by defining HDF5_PLUGIN_PATH to point to the build kit shared library directory:

    HDF5_PLUGIN_PATH=$(SOLIB); export HDF5_PLUGIN_PATH;

    In most cases that should be sufficient to allow code to read HDF5 files with datasets compressed with this filter.

    In order to write files that use this filter, several relevant values must first be stored into an unsigned int array, cd_values. The header, cbf_hdf5_filter.h, defines the follwing symbolic values for the indices of this array:

    symbolvaluemeaning
    CBF_H5Z_FILTER_CBF_NELMTS 11size of cd_values
    CBF_H5Z_FILTER_CBF_COMPRESSION 0one of the compressions (see 3.2.2)
    CBF_H5Z_FILTER_CBF_RESERVED 1reserved for future use, should be set to zero
    CBF_H5Z_FILTER_CBF_BINARY_ID 2binary ID of the array (default 1)
    CBF_H5Z_FILTER_CBF_ELSIZE 3element size in octets
    CBF_H5Z_FILTER_CBF_ELSIGN 41 if signed, 0 if unsigned
    CBF_H5Z_FILTER_CBF_REAL 51 if a real array, 0 if an integer array
    CBF_H5Z_FILTER_CBF_DIMOVER 6the total number of elements in the array
    CBF_H5Z_FILTER_CBF_DIMFAST 7the fast dimension
    CBF_H5Z_FILTER_CBF_DIMMID 8the middle dimension
    CBF_H5Z_FILTER_CBF_DIMSLOW 9the slow domension
    CBF_H5Z_FILTER_CBF_PADDING 10the padding

    Only chunked data may be written using this filter. The recommended chunk size is a single image. The filter writes the chunks using the imgCIF binary section format described in section 3.2.1 including the MIME header. If each chunk is the size of an image, programs such as XDS can use the patterns of the MIME header to skip directly to a frame even in a complex HDF5 file. Typical code to write such chunks would first define the cd_values array and an array of chunk dimensions and create the properties to be used in creating a dataset, as in

        unsigned int cd_values[CBF_H5Z_FILTER_CBF_NELMTS];
        hsize_t chunk[3];
        hid_t valspace;
        chunk[0] = 1;
        chunk[1] = dimmid;
        chunk[2] = dimfast;
        cd_values[CBF_H5Z_FILTER_CBF_COMPRESSION] = compression;
        cd_values[CBF_H5Z_FILTER_CBF_RESERVED]    = 0;
        cd_values[CBF_H5Z_FILTER_CBF_BINARY_ID]   = id;
        cd_values[CBF_H5Z_FILTER_CBF_PADDING]     = padding;
        cd_values[CBF_H5Z_FILTER_CBF_ELSIZE]      = (bits+7)/8;
        cd_values[CBF_H5Z_FILTER_CBF_ELSIGN]      = sign;
        cd_values[CBF_H5Z_FILTER_CBF_REAL]        = realarray;
        cd_values[CBF_H5Z_FILTER_CBF_DIMFAST]     = dimfast;
        cd_values[CBF_H5Z_FILTER_CBF_DIMMID]      = dimmid;
        cd_values[CBF_H5Z_FILTER_CBF_DIMSLOW]     = dimslow;
        valprop = H5Pcreate(H5P_DATASET_CREATE);
        H5Pset_chunk(valprop,3,chunk);
        H5Pset_filter(valprop,CBF_H5Z_FILTER_CBF,H5Z_FLAG_OPTIONAL,CBF_H5Z_FILTER_CBF_NELMTS,cd_values);
    

    4. Installation

    CBFlib should be built on a disk with at least 400 megabytes of free space. CBFlib-0.9.2.11.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_0.9.2.11 (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]}|{I|nIbble_offset}|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]\
          [-5 {r|w|rw|rn|wn|rwn|n[oH5]}\
          [-O] \
          [input_cif] [output_cbf]
    
      the options are:
    
           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, nIbble 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                              
                                                                             
           -5 hdf5mode specifies whether to read and/or write in hdf5 mode   
              the n parameter will cause the CIF H5 datablock to be deleted  
              on both read and write, for both CIF, CBF and HDF5 files       
                                                                             
           -O when in -5 w (hdf5 write) mode, -O forces the use of opaque    
              objects for CBF binaries                                       
                                                                             
                                                                             
    
    

    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:

    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:

    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
      
    

    minicbf2nexus

    This program takes some minicbf files describing a single scan and axis configuration settings for them and creates a nexus file containing the same data. As this is an early version of the program it lacks a lot of useful functionality and should not be assumed to be stable.

    It currently takes several command line arguments:

    An example, from the test scripts, is:

    minicbf2nexus -c zlib -C config X4_test_1.cbf X4_test_2&3.cbf X4_test_4.cbf X4_test_5.cbf -o minicbf.h5

    Where test files 1, 4 & 5 are each single-image miniCBF files and test file 2 & 3 is created by 'cat'ing together two single-image miniCBF files

    The config file used for this example is:

    # some sample config settings for a miniCBF file
    
    map Start_angle to CBF_axis_omega
    map Phi to CBF_axis_phi
    map Kappa to CBF_axis_kappa
    
    Sample depends-on CBF_axis_phi
    
    CBF_axis_phi vector [1 0 0] depends-on CBF_axis_kappa
    CBF_axis_kappa vector [0 1 0] depends-on .
    CBF_axis_omega vector [0 0 0]
    

    Text from any # character to the end of the line is ignored as a comment.

    Axes are declared by the map keyword as the name of the axis in the minicbf file, which must match exactly, followed by the keyword to and then the name that will be given to the axis in the resulting nexus file. Each axis is treated as a rotation axis and should have a vector which defines the axis of rotation in the 3D coordinate frame used by nexus, this should be 3 numbers within square brackets separated by spaces and does not need to be normalised. Each axis may also depend on a nother axis by using the keyword depends-on folowed by the name of the nexus axis it depends on, or . if it does not depend on another axis, omitting a dependency as shown on the final line of the example above is not recommended as it will eventually be a fatal error. The vector and depends-on declarations do not need to be on the same line.

    The Sample keyword is used to define a dependency for the sample being scanned and should be followed by a depends-on declaration which defines the name of the nexus axis that the sample depends on.

    The final line of the config file should be blank to allow for some simple integrity tests.

    A continuous chain of dependencies should be formed from the sample to the nexus coordinate system, otherwise there is insufficient information available to properly describe the orientation of the sample. This will be enforced in later versions, with a fatal error if insufficient information is provided.

    cbf2nexus

    This program takes some CBF files describing a single scan and converts them to a single NeXus file containing the same data.

    It currently takes several command line arguments:

    An example, from the test scripts, is:

    cbf2nexus -c zlib adscconverted.cbf adscconverted.cbf -o cbf.zlib.h5

    This creates a single NeXus file containing two copies of the 'adscconverted' CBF file.

    nexus2cbf

    This program converts a single frame of data from a nexus file to a cbf file with a given name. The primary purpose of this program is to help verify that data can be recovered after being converted to NeXus format, to check that it hasn't been lost or mangled.

    It currently takes several command line arguments:

    testhdf5

    This program runs a set of unit tests on the HDF5 abstraction layer. These are designed to ensure everything is working correctly, to help locate bugs and prevent regressions. A short summary will be printed detailing the number of tests passed, the number of tests failed and the number of components skipped. If any tests fail or are skipped then some additional output should be produced to help identify the cause of the error so that it is easier to fix.

    The program does not take any command-line arguments, and creates a file called testfile.h5 in its working directory for use in the tests.

    testulp

    This program runs a set of unit tests on the ULP comparison functions. These are designed to ensure everything is working correctly, to help locate bugs and prevent regressions. A short summary will be printed detailing the number of tests passed, the number of tests failed and the number of components skipped. If any tests fail or are skipped then some additional output should be produced to help identify the cause of the error so that it is easier to fix.

    The program does not take any command-line arguments.




    Updated 27 April 2014. Contact: