CBFlib ChangeLog
An API for CBF/imgCIF
Crystallographic Binary Files with ASCII Support
Version 0.9.2
12 February 2011
by
Paul J. Ellis
Stanford Synchrotron Radiation Laboratory
and
Herbert J. Bernstein
Bernstein + Sons
yaya at bernstein-plus-sons dot com
(c) Copyright 2006, 2007, 2008, 2011 Herbert J. Bernstein
----------------------------------------------------------------------
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.
----------------------------------------------------------------------
Version History
Version Date By Description
0.1 Apr. 1998 PJE This was the first CBFlib release.
It supported binary CBF files using
binary strings.
0.2 Aug. 1998 HJB This release added ascii imgCIF
support using MIME-encoded binary
sections, added the option of MIME
headers for the binary strings was
well. MIME code adapted from mpack
1.5. Added hooks needed for DDL1-style
names without categories.
0.3 Sep. 1998 PJE This release cleaned up the changes
made for version 0.2, allowing
multi-threaded use of the code, and
removing dependence on the mpack
package.
0.4 Nov. 1998 HJB This release merged much of the
message digest code into the general
file reading and writing to reduce the
number of passes. More consistency
checking between the MIME header and
the binary header was introduced. The
size in the MIME header was adjusted
to agree with the version 0.2
documentation.
0.5 Dec. 1998 PJE This release greatly increased the
speed of processing by allowing for
deferred digest evaluation.
0.6 Jan. 1999 HJB This release removed the redundant
information (binary id, size,
compression id) from a binary header
when there is a MIME header, removed
the unused repeat argument, and made
the memory allocation for buffering
and tables with many rows sensitive to
the current memory allocation already
used.
0.6.1 Feb. 2001 HP (per This release fixed a memory leak due
HJB) to misallocation by size of cbf_handle
instead of cbf_handle_struct
0.7 Mar. 2001 PJE This release added high-level
instructions based on the imgCIF
dictionary version 1.1.
0.7.1 Mar. 2001 PJE The high-level functions were
revised to permit future expansion to
files with multiple images.
0.7.2 Apr. 2001 HJB This release adjusted cbf_cimple.c
to conform to cif_img.dic version
1.1.3
0.7.2.1 May 2001 PJE This release corrected an if nesting
error in the prior mod to
cbf_cimple.c.
0.7.3 Oct. 2002 PJE This release modified cbf_simple.c
to reorder image data on read so that
the indices are always increasing in
memory (this behavior was undefined
previously).
0.7.4 Jan 2004 HJB This release fixes a parse error for
quoted strings, adds code to get and
set character string types, and
removes compiler warnings
0.7.5 Apr 2006 HJB This release cleans up some compiler
warnings, corrects a parse error on
quoted strings with a leading blank as
adds the new routines for support of
aliases, dictionaries and real arrays,
higher level routines to get and set
pixel sizes, do cell computations, and
to set beam centers, improves support
for conversion of images, picking up
more data from headers.
0.7.6 Jul 2006 HJB This release reorganizes the kit
into two pieces:
CBFlib_0.7.6_Data_Files and
CBFlib_0.7.6. An optional local copy
of getopt is added. The 1.4 draft
dictionary has been added. cif2cbf
updated to support vcif2 validation.
convert_image and cif2cbf updated to
report text of error messages.
convert_image updated to support tag
and category aliases, default to adxv
images. convert_image and img updated
to support row-major images. Support
added for binning. API Support added
for validation, wide files and line
folding. Logic changed for beam center
reporting. Added new routines:
cbf_validate, cbf_get_bin_sizes,
cbf_set_bin_sizes,
cbf_find_last_typed_child,
cbf_compose_itemname,
cbf_set_cbf_logfile,
cbf_make_widefile, cbf_read_anyfile,
cbf_read_widefile,
cbf_write_local_file,
cbf_write_widefile, cbf_column_number,
cbf_blockitem_number, cbf_log,
cbf_check_category_tags,
cbf_set_beam_center
0.7.7 February 2007 HJB This release reflects changes for
base 32K support developed by G.
Darakev, and changes for support of
reals, 3d arrays, byte_offset
compression and J. P. Abrahams packed
compression made in consultation with
(in alphabetic order) E. Eikenberry,
A. Hammerley, W. Kabsch, M. Kobas, J.
Wright and others at PSI and ESRF in
January 2007, as well accumulated
changes fixing problems in release
0.7.6.
0.7.7.1 February 2007 HJB This release is a patch to 0.7.7 to
change the treatment of the byteorder
parameter from strcpy semantics to
return of a pointer to a string
constant. Our thanks to E. Eikenberry
for pointing out the problem.
0.7.7.2 February 2007 HJB This release is a patch to 0.7.7.1
to add testing for JPA packed
compression and to respect signs
declared in the MIME header.
0.7.7.3 April 2007 HJB This release is a patch to 0.7.7.3
to add f90 support for reading of CBF
byte-offset and packed compression, to
fix problems with gcc 4.4.1 and to
correct errors in multidimensional
packed compression.
0.7.7.4 May 2007 HJB Corrects in handling SLS detector
mincbfs and reorder dimensions versus
arrays for some f90 compilers as per
H. Powell.
0.7.7.5 May 2007 HJB Fix to cbf_get_image for bug
reported by F. Remacle, fixes for
windows builds as per J. Wright and F.
Remacle.
0.7.7.6 Jun 2007 HJB Fix to CBF byte-offset compression
writes, fix to Makefiles and m4 for
f90 test programs to allow adjustable
record length.
0.7.8 Jul 2007 HJB Release for full support of SLS data
files with updated convert_minicbf,
and support for gfortran from gcc 4.2.
0.7.8.1 Jul 2007 HJB Update to 0.7.8 release to fix
memory leaks reported by N. Sauter and
to update validation checks for recent
changes.
0.7.8.2 Dec 2007 CN, HJB Update to 0.7.8.1 to add ADSC jiffie
by Chris Nielsen, and to add ..._fs
and ..._sf macros.
0.7.9 Dec 2007 CN, HJB Identical to 0.7.8.2 except for a
cleanup of deprecated examples, e.g.
diffrn_frame_data
0.7.9.1 Jan 2008 CN, HJB Update to 0.7.8.2 to add inverse
ADSC jiffie by Chris Nielsen, to clean
up problems in handling maps for
RasMol.
0.8.0 Jul 2008 GT, HJB Cleanup of 0.7.9.1 to start 0.8
series.
0.8.1 Jul 2009 EZ, CN, Release with EZ's 2008 DDLm support
PC, GW, using JH's PyCifRW, also cbff f95
JH, HJB wrapper code, PC's java bindings.
0.9.1 Aug 2010 PC, EE, Release with EE's Dectris template
JLM, NS, software, also with vcif3, new
EZ, HJB arvai_test, sequence_match.
0.9.2 Feb 2011 PC, EE, New default release with updated
JLM, NS, pycbf, tiff support, removal of
EZ, HJB default use of PyCifRW to avoid Fedora
license issue.
----------------------------------------------------------------------
Release 0.9.2, Herbert J. Bernstein, 12 February 2011
Source File Change
Makefile.m4, Makefiles Changes for libtiff and tiff2cbf. Create a
separate setup.py for MINGW. Allow
CBF_DONT_USE_LONG_LONG variable to control
Makefiles. Disable default use of PyCifRW
because of Fedora concerns about PyCifRW
license issues. Force use of long long for
SWIG. Update Makefiles to run
changtestcompression. Update pycbf build.
cbf_template_t.c Don't use /tmp for dectris template code. Add
EE's change for DLS signs
cbf_copy.c Fix cbf_copy.c to handle not using long long
correctly
jcbf.i Move cbf.i to jcbf directory.
cbf_byte_offset.h,
cbf_canonical.h, Implement P. Chang's fast byte-offset
cbf_compress.h, decompress, but with hooks to run on machines
cbf_packed.h, without long long support. Fix bad mask, fix
cbf_predictor.h, sign extension for MINGW and other systems in
cbf_uncompressed.h, cbf.c, which long long is not used. Fix error in
cbf_binary.c, mpint_shift logic causing erroneous sign Add
cbf_byte_offset.c, changes in the compression infrastructure by P.
cbf_canonical.c, Chang to make the compressed size available on
cbf_compress.c, decompression. Extend cbf_canonical to support
cbf_packed.c, long long and double. Correct cbf_packed for
cbf_predictor.c, elsize 8 data.
cbf_uncompressed.c, cbff.c
cbfdetectorwrappers.i, Update pycbf for 0.9 release Add
cbfgenericwrappers.i, cbf_get_detector_axis_slow,
cbfgoniometerwrappers.i, cbf_get_detector_axis_fast,
cbfhandlewrappers.i, cbf_get_detector_axes,
make_pycbf.py, pycbf.py, cbf_get_detector_axes_fs, cbf_get_detector_sf,
pycbf_test2.py, and changes for pycbf wrapper
pycbf_wrap.c, cbf_simple.c
cbf2adscimg_sub.c Fix buffer overflow
cif_img_1.6.3_26Aug10.dic,
cif_img_1.6.3_26Aug10.html
Add variant category and
tags and
diffrn_scan_frame_monitor
----------------------------------------------------------------------
Release 0.9.1, P. Chang, E. Eikenberry, J. Lewis Muir, N. Sauter, E. Zlateva,
Herbert J. Bernstein, 15 August 2010
Source File Change
cbf_simple.c Fix nested axis handling.
cbf_template_t.c Add E.E.'s Dectris template software. Change to
C-style comments.
Makefile.m4, Add DMALLOC hooks.
Makefiles
arvai_test.c,
seqmatchsub.c,
seqmatchsub.h,
sequence_match.c, Add arvai_test and sequence_match examples. Transfer
cbf_copy.h, copy logic from cib2cbf into cbf_copy.c
Makefile.m4,
cbf_ascii.c,
cbf_copy.c
cbf.h,
cbf_ascii.h,
cbf_file.h, As per request by J. Lewis Muir, direct all warning
cbf_write.h, messages through cbf_log or new cbf_flog, so such
cbff.h, cbf.c, messages can all be suppressed by setting the logfile
cbf_ascii.c, to NULL
cbf_file.c,
cbf_lex.c,
cbf_write.c
cbf_byte_offset.c, Fix to byte-offset compression for 16 bit data with a
cbf_file.c delta that looks like a flag. Fix to setting/getting
file position when there is no stream. Fix incorrect
sign extension test as per N. Sauter.
convert_minicbf.c Allow for changes in miniheader and report
unrecognized lines but continue. Also allow S/N instead
of SN
Makefile.m4,
Makefiles, As per P. Chang, decouple CBF_UNDEFINED error return
Java.txt, from CBF_UNDEFINED node type by defining CBF_UNDEFNODE
testcbf.java, (rather than PC's CBF_UNDEFINEDNODE)
cbf.c
drel_prep.py,
drel_yacc.py,
cif2cbf.c, cbf.h,
cbf.c,
cbf_ascii.c, vcif 3 release.
cbf_lex.c,
cbf.stx.y,
cbf_getopt.c,
cbf_stx.c
cbf.h, cbf.c Add function cbf_set_column_name
----------------------------------------------------------------------
Release 0.8.1, E. Zlateva, C. Neilsen, P. Chang, G. Winter, J. Hester, Herbert
J. Bernstein, 24 July 2009
Source File Change
cbf.h, cbf_stx.h,
cbf_tree.h, cbf.c,
cbf.stx.y, As per EZ, Add DDLm support, parsing of function
cbf_lex.c, definitions. Add auto download of J. Hester's PyCifRW
cbf_stx.c, and PLY
Makefile.m4,
Makefiles
cbf_getopt.c Correct a memory leak and ensure correct handling of
unspecified options when a '-' is given on the option
string.
CBFlib.html, As per G. Winter correct documentation of byte-offset
CBFlib.txt algorithm to refer to hex 80 not hex F0.
cbf_getopt.h,
cbf_getopt.c,
Makefile.m4,
Makefiles, Introduce cbf_getopt.h, cbf_getopt.c, remove use of
cif2cbf.c, getopt
convert_image.c,
convert_minicbf.c,
img2cif.c
Java.txt,
testcbf.c, P. Chang's java bindings
testcbf.java,
Makefile.m4, cbf.i
libtool directory Add a libtool build directory for future use of
shared libraries.
cif2cbf.c Add test for construct_detector to cif2cbf. Fix
getopt option string.
cif_tree.h Add DDLm bracket types for nodes
adscimg2cbf.c, Apply mods to adscimg2cbf by C. Nielsen: Add new
adscimg2cbf_sub.c command line options: --beam_center_from_header, Figure
out beam center from ADSC header information (default);
--beam_center_mosflm, Beam center in ADSC header:
MOSFLM coordinates; --beam_center_ulhc, Beam center in
ADSC header: origin: upper left hand corner of
image.(HKL mm); --beam_center_llhc, Beam center in ADSC
header: origin: lower left hand corner of image.(adxv
mm)
cbff.h, cbff.c Add src/cbff.c and include/cbff.h as start of full
f95 wrapper for C code
----------------------------------------------------------------------
Release 0.8.0, G. Todorov, Herbert J. Bernstein, 21 July 2008
Source File Change
adscimg2cbf_sub.c, Patch to deal with gcc 4 optimization error in get_bo
adscimg2cbf_sub.c Replaced with call to cbf_get_local_integer_byte_order.
cbf.c, cbf.h, Clean up spacing; trim trailing blanks in text
cbf_ascii.c, fields; validate DDLm types. Add MSG_DIGESTWARN. Update
cbf_file.c, spacing. Fix includes for regex use. Fixes on achar and
cbf_lex.c, anchar and element. Added cbf_check_type_contents
cbf_write.c function that will verify ddlm types based on regular
expressions. Fix handling for bracketed unquoted words
and handle more DDLm tags. Fix scan of DDLm bracketed
constructs with embedded quotes. Pick up item names in
DDLm save frames. Fix cif2cbf handling of bracketed
constructs in dictionaries. Updates to bracketed
construct parse and output logic. Update write logic
for bracketed constructs with folding.
cbf_set_tag_category() code fixed. Change internal
routine cbf_read_anyfile and add new user routine
cbf_read_buffered_file to support pre-read of input
files and memory-only files. Add new routines
cbf_io_buffersize and cbf_reset_in_bits and change read
logic to allow buffered reads.
----------------------------------------------------------------------
Release 0.7.9.1, Chris Nielsen, Herbert J. Bernstein, 24 January 2008
Source File Change
cbf2adscimg.c Last minutes fixes on release: Put missing byte swap
cbf2adscimg_sub.c in cbf2adscimg.c for when byte orders differ. Bypass
problems with gcc optimization, and handle case then
array header is there but invalid.
.symlinks Update version to 0.7.9
.undosymlinks
Makefile.m4 Update for CN's jiffies, and testing with MD5
Makefile, signatures only
Makefile_AIX ...
cbf2adscimg.c New inverse jiffie by Chris Nielsen of ADSC to
cbf2adscimg_sub.c convert CBF files created by convert_image or
adscimg2cbf to ADSC detector images. This version
depends on the header extract planted by convert_image
or adscimg2cbf.
cbf_byte_offset.c Fix handling of byte offset compression when the data
does not compress.
cbf_codes.c Fix 32K encoding big-endian test as per Ladislav
Michnovic .
cbf_packed.c Correct mishandling of 64 bit data.
cbf_uncompressed.c Remove redundant initialization of
unsigned_char_data.
cbf_write.c.c Fix conflicting uses of variable column by
introducing separate variable xcol.
README.html README Update to version 0.7.9 directory structure and
programs.
cbf.c Fix local sensitivity of cbf_get_doublevalue and
cbf_set_doublevalue so "." will be accepted and written
as the decimal point in locales that use ",".
----------------------------------------------------------------------
Release 0.7.9, Chris Nielsen, Herbert J. Bernstein, 30 December 2007
Source File Change
Makefiles and test data Change test cases to avoid deprecated features.
----------------------------------------------------------------------
Release 0.7.8.2, Chris Nielsen, Herbert J. Bernstein, 25 December 2007
Source File Change
adscimg2cbf.c adscimg2cbf_sub.c New jiffie by Chris Nielsen of ADSC
to convert ADSC detector images to
CBF.
cbf.h cbf_byte_offset.h, cbf_compress.h, Add _fs and _sf versions of
cbf_read_mime.h, cbf_simple.h cbf_get_arrayparameters_wdims,
cbf_get_integerarrayparameters_wdims,
cbf_get_realarrayparameters_wdims,
cbf_set_integerarray_wdims,
cbf_set_realarray_wdims,
cbf_compress_byte_offset,
cbf_compress, cbf_decompress,
cbf_parse_mimeheader,
cbf_get_pixel_size,
cbf_set_pixel_size,
cbf_get_image_size, cbf_get_image,
cbf_get_real_image,
cbf_get_3d_image_size,
cbf_get_3d_image,
cbf_get_real_3d_image, cbf_set_image,
cbf_set_real_image, cbf_set_3d_image,
cbf_set_real_3d_image,
cbf_get_map_array_id,
cbf_get_map_segment_size,
cbf_get_map_segment,
cbf_get_map_segment_mask,
cbf_get_real_map_segment,
cbf_get_real_map_segment_mask,
cbf_set_map_segment,
cbf_set_map_segment_mask,
cbf_set_real_map_segment,
cbf_set_real_map_segment_mask,
cbf_get_3d_array_size,
cbf_get_3d_array, cbf_set_3d_array,
cbf_get_beam_center,
cbf_set_beam_center,
cbf_set_reference_beam_center,
cbf_get_pixel_coordinates,
cbf_get_pixel_normal,
cbf_get_pixel_area,
cbf_get_inferred_pixel_size
cbf_alloc.h Add prototype of cbf_free_text.
cbf_binary.h Add prototype of cbf_check_digest.
cbf_canonical.h Add definitions of
cbf_compress_node and
cbf_compress_data, and prototypes of
cbf_make_compressdata,
cbf_free_compressdata,
cbf_initialise_compressdata,
cbf_put_table, cbf_get_table,
cbf_put_stopcode, cbf_insert_node,
cbf_append_node, cbf_order_node,
cbf_create_list, cbf_reduce_list,
cbf_generate_codelengths,
cbf_reverse_bitcodes,
cbf_generate_canonicalcodes,
cbf_compare_bitcodes,
cbf_construct_tree, cbf_setup_decode,
cbf_count_bits, cbf_get_code,
cbf_put_code and cbf_count_values.
cbf_simple.h Add prototypes of
cbf_get_detector_id and
cbf_gregorian_julian.
cbf_string.c, cbf_string.h Add cbf_swab function for MS
windows and other machines that do
not provide swab.
cbf.c, cbf_binary.c, cbf_byte_offset.c, Change dim1, dim2, dim3 to dimfast,
cbf_canonical.c, cbf_compress.c, dimmid, dimslow, ndim1, ndim2 to
cbf_lex.c, cbf_packed.c, cbf_predictor.c, ndimslow, ndimfast. machines that do
cbf_read_mime.c, cbf_simple.c, not provide swab.
cbf_uncompressed.c, cbf_write_binary.c
cif2c.c Make declaration of xciftmp
conditional to avoid compiler
warnings.
convert_image.c Add code to check variations on
pixel_size functions.
convert_minicbf.c Add second quick exit option (-Q).
Improve error reporting. Update for
most recent SLS miniheader.
getopt.c Fix some compiler warnings.
Makefile.m4 add adscimg2cbf support
template_pilatus6m_2463x2527.cbf Update pilatus6m template for
correct detector axis definitions,
better comments and to list all
categories used by SLS.
template_adscquantum315_3072x3072_rev.cbf New, corrected ADSC Quantum 315
template.
----------------------------------------------------------------------
Release 0.7.8.1, Chris Nielsen, Herbert J. Bernstein, 28 July 2007
Source File Change
cbf.c Rework cbf_free_handle to ensure release of memory
from root, not current position. Rework
cbf_read_anyfile to ensure close of file stream on all
exit cases. Fix save frame code in cbf_validate to
restart counts on each save frame. Add name, idname and
aliasname types from latest DDL2 dictionary.
cbf_alloc.c, Add cbf_free_text to avoid type punning warnings from
cbf_alloc.h gcc 4. Add memory debug based on adding
-DCBFLIB_MEM_DEBUG to CFLAGS.
cbf_simple.c Add code to ensure against memory leaks when working
with a detector or positioner object.
cbf.stx.y, Add calls to cbf_undo_links and cbf_free_text to
cbf_stx.c clean up memory leaks in parser. Add validation calls
to mark end of save frames.
cbf_tree.c, Add cbf_undo_links to recover memory from links used
cbf_tree.h to rotate among columns of a table. Rework
cbf_free_node to avoid memory leaks.
cbf_uncompressed.c Add #define __USE_XOPEN to avoid a warning on use of
swab on some systems.
sauter_test.C Add sauter_test to stress test for memory leaks. On
Makefile.m4 make install, place cbf.h and cbf_simple.h into include
directory.
----------------------------------------------------------------------
Release 0.7.8, Herbert J. Bernstein, 8 July 2007
Source File Change
cbf_simple.c Update handling of both beam center and reference beam
center to allow for units and new dictionary.
convert_minicbf.c Add code to handle data in
_array_data.header-contents. Clean up error handling,
map all SLS tags. Add -Q option to convert old SLS
comment format to new text field format.
Makefile,
Makefile_AIX, As per ND add Makefile_LINUX_gcc42 and
Makefile_LINUX, Makefile_OSX_gcc42 to handle gfortran 4.2 problems.
Makefile_OSX
----------------------------------------------------------------------
Release 0.7.7.6, Herbert J. Bernstein, 30 June 2007
Source File Change
cbf_codes.c Fix memory leaks in base32k encoding by G. Darakev.
cbf_byte_offset.c Fix in handling 32 bit offsets in the fast write code,
which were incorrectly handled as 16 bit offsets.
Makefile, Add M4FLAGS variable to control m4 expansion of f90
Makefile_AIX, test programs with different record lengths. For g95,
Makefile_LINUX, the record length must not be larger than the padding.
Makefile_OSX
----------------------------------------------------------------------
Release 0.7.7.5, Herbert J. Bernstein, 9 May 2007
Source File Change
cbf_codes.c Change from use of bzero to memset and remove include
of strings.h
cbf_codes.c Change from use of bzero to memset and remove include
of strings.h
cbf_simple.c Fix ordering of dimensions in cbf_get_3d_array_size
and handling of non-zero binary ids to fix problems
with cbf_get_image and cbf_get_image_size
cbf_uncompressed.c Add include of unistd.h for use of swab on more
systems
Makefile Introduce $(TIME) variable for time command so it can
be suppressed in windows
fcb_read_bits.m4 Changes for g95 compatibility.
cif2c.c, Make use of mkstemp conditional on NOMKSTEMP. Make
cif2cbf.c, etc. use of /tmp conditional on NOTMPDIR.
----------------------------------------------------------------------
Release 0.7.7.4, Herbert J. Bernstein, 6 May 2007
Source File Change
cbf_simple.c Fix ordering of dimensions in cbf_set_3d_array.
cbf_uncompressed.c Add include of ctype.h to provide prototype for
toupper.
convert_image.c Enable -p option for non-standard templates; correct
handling of seconds in timestamps.
convert_minicbf.c Enable code for timestamp, exposure time,
comment-style header.
fcb_packed.m4 As per H. Powell, move declarations for dimensions
before declarations of arrays.
fcb_read_image.m4 As per H. Powell, move declarations for dimensions
before declarations of arrays.
fcblib_defines.m4 As per H. Powell, move declarations for dimensions
before declarations of arrays.
----------------------------------------------------------------------
Release 0.7.7.3, Herbert J. Bernstein, 3 April 2007
Source File Change
Makefile Add m4 directory to build f90 sources. Add .f90
routines to src and examples. Add libfcb.a to lib.
Add tests for f90 routines to extra tests.
testflat.c Add support for 3D test.
testflatpacked.c Add support for 3D test.
cbf_binary.c Correct dim2,dim2 to be dim1,dim2 in
check_digest.
cbf_packed.c Correct JPA pointer logic for 3D case. Work
around compiler problems with handling of sign
bits
fcb_exit_binary.m4 New m4 macro file to build fcb_exit_binary.f90 a
routine to skip from the end of a binary to the
end of the text field.
fcb_next_binary.m4 New m4 macro file to build fcb_next_binary.f90 a
routine to skip to the start of the next binary.
fcb_open_cifin.m4 New m4 macro file to build fcb_open_cifin.f90 a
routine to open a cbf file.
fcb_packed.m4 New m4 macro file to build fcb_packed.f90 a
routine to uncompress JPA packed binaries.
fcb_read_bits.m4 New m4 macro file to build fcb_read_bits.f90 a
routine to read an arbitrary number of bits as an
integer.
fcb_read_image.m4 New m4 macro file to build fcb_read_image.f90 a
set of routines to read a byte offset or packed
image
fcb_read_xds_i2.m4 New m4 macro file to build fcb_read_xds_i2.f90 a
routine to read a single xds I2 image.
fcblib_define.m4 New m4 macro file of common definitions for all
f90 code
test_fcb_read_image.m4 New m4 macro file of build
test_fcb_read_image.f90 a test program for the f90
routines.
test_xds_binary.m4 New m4 macro file of build test_xds_binary.f90 a
test program for the f90 routines.
fcb_atol_wcnt.f90 f90 code to convert a string to an integer.
fcb_ci_strncmparr.f90 f90 code to do a case-insensitive string
comparison
fcb_nblen.f90 f90 code to do test the non-blank length of a
string
fcb_read_byte.f90 f90 code to read a byte
fcb_read_line.f90 f90 code to read a line
fcb_skip_whitespace.f90 f90 code to skip MIME whitespace
----------------------------------------------------------------------
Release 0.7.7.2, Herbert J. Bernstein, 27 February 2007
Source File Change
Makefile Add testflatpacked build to extra test dependencies.
testflat.c Add more test cases.
testflatpacked.c Add version of testflat for packed compression.
cbf_binary.c Add recovery of sign from mime header.
cbf_byte_offset.c Change limit logic to simple mask and remove overflow
report.
cbf_packed.c Change limit logic to simple mask and remove overflow
report.
cbf_uncompressed.c Change limit logic to simple mask and remove overflow
report.
----------------------------------------------------------------------
Release 0.7.7.1, Herbert J. Bernstein, 25 February 2007
Source File Change
Makefile Add testflat build to extra test dependencies.
CBFlib.html Add descriptions of
cbf_get_integerarrayparameters_wdims,
cbf_get_realarrayparameters_wdims,
cbf_set_integerarray_wdims, cbf_set_realarray_wdims
cif2cbf.c Change to use of byteorder as a pointer to a
constant string, rather than as a local copy of a
string.
testflat.c Add report of byteorder, dim1, dim2, dim2, padding.
cbf.h, Change prototypes for all functions that return
cbf_binary.h, byteorder from char * byteorder to const char **
cbf_byte_offset.h, byteorder. Change prototypes of all functions that set
cbf_canonical.h, byteorder from char * byteorder to const char *
cbf_compress.h, byteorder
cbf_packed.h,
cbf_predictor.h,
cbf_read_mime.h,
cbf_uncompressed.h
cbf.c, Change signatures for all functions that return
cbf_binary.c, byteorder from char * byteorder to const char **
cbf_byte_offset.c, byteorder. Change prototypes of all functions that set
cbf_canonical.c, byteorder from char * byteorder to const char *
cbf_compress.c, byteorder, and make the matching changes in all calls.
cbf_lex.c,
cbf_packed.c,
cbf_predictor.c,
cbf_read_mime.c,
cbf_uncompressed.c,
cbf_write_binary.c
----------------------------------------------------------------------
Release 0.7.7, Herbert J. Bernstein, 19 February 2007
Source File Change
cif2cbf.c Add support for byte offset, packed version 2 and
flat compression, and binary section padding. Add
support for base-32K encoding. Allow command line
compression to override compression_type in the file
and to set compression_type_flag.
convert_image.c Add support for new -R and -F flags, for use of
reference beam center and flat packed compression
respectively.
cbf.h Add constants CBF_PACKED_V2 for packed version 2
compression, CBF_UNCORRELATED_SECTIONS for uncorrelated
sections in packed compression, CBF_FLAT_IMAGE for
original CBFlib packed compression, PAD_1K, PAD_2K and
PAD_4K for trailing pad on binary sections, ENC_BASE32K
for base 32K encoding. Fix bad code in DEBUG mode for
failnez macros. Add prototypes for
cbf_get_arrayparameters_wdims,
cbf_get_integerarrayparameters_wdims,
cbf_get_realarrayparameters_wdims,
cbf_set_integerarray_wdims, cbf_set_realarray_wdims,
cbf_mpint_load_acc, cbf_mpint_store_acc,
cbf_mpint_clear_acc, cbf_mpint_increment_acc,
cbf_mpint_decrement_acc, cbf_mpint_negate_acc,
cbf_mpint_add_acc, cbf_mpint_rightshift_acc,
cbf_mpint_leftshift_acc.
cbf_binary.h Update prototypes for cbf_get_bintext,
cbf_set_bintext, cbf_set_binary, cbf_binary_parameters,
cbf_get_binary to carry byteorder, dimensions and
padding.
cbf_byte_offset.h Update prototypes for cbf_compress_byte_offset,
cbf_decompress_byte_offset to carry byteorder,
dimensions and padding.
cbf_canonical.h Update prototypes for cbf_compress_canonical,
cbf_decompress_canonical to carry byteorder, dimensions
and padding.
cbf_codes.h Add prototypes for base 32K encoding: cbf_tobase32k,
cbf_encode32k_bit_op, cbf_isBigEndian, cbf_endianFix,
cbf_frombase32k, cbf_decode32k_bit_op.
cbf_compress.h Update prototypes for cbf_compress, cbf_decompress
to carry byteorder, dimensions and padding.
cbf_packed.h Update prototypes for cbf_compress_packed,
cbf_decompress_packed to carry byteorder, dimensions
and padding.
cbf_predictor.h Update prototypes for cbf_compress_predictor,
cbf_decompress_predictor to carry byteorder, dimensions
and padding.
cbf_read_mime.h Update prototype for cbf_parse_mimeheader to carry
byteorder, dimensions and padding.
cbf_simple.h Add prototypes for cbf_get_3d_array_size,
cbf_get_3d_array, cbf_get_3d_image_size,
cbf_get_3d_image, cbf_get_map_array_id,
cbf_get_map_segment_mask, cbf_get_map_segment_size,
cbf_get_map_segment, cbf_get_real_3d_image,
cbf_get_real_map_segment,
cbf_get_real_map_segment_mask, cbf_set_3d_array,
cbf_set_3d_image, cbf_set_map_segment,
cbf_set_map_segment_mask, cbf_set_real_3d_image,
cbf_set_real_map_segment,
cbf_set_real_map_segment_mask.
cbf_uncompressed.h Update prototypes for cbf_compress_none,
cbf_decompress_none to carry byteorder, dimensions and
padding.
Makefile Update version and tests to work against data files
in CBFlib_0.7.7_Data_Files.
cbf.c Remove compiler warnings on signedness and type
punned pointers. Fix bug in detection of local real
format. Add base32K support. Fix inverted test in value
range checking. Add new routines
cbf_get_arrayparameters_wdims,
cbf_get_integerarrayparameters_wdims,
cbf_get_realarrayparameters_wdims,
cbf_set_integerarray_wdims, cbf_set_realarray_wdims,
cbf_mpint_load_acc, cbf_mpint_store_acc,
cbf_mpint_clear_acc, cbf_mpint_increment_acc,
cbf_mpint_decrement_acc, cbf_mpint_negate_acc,
cbf_mpint_add_acc, cbf_mpint_rightshift_acc,
cbf_mpint_leftshift_acc.
cbf.stx.y Temporarily change to use of YYSTYPE argument type to
remove an error when compiling under on MS Windows. A
better solution is needed./
cbf_binary.c Update cbf_get_bintext, cbf_set_bintext,
cbf_set_binary, cbf_binary_parameters, cbf_get_binary
to carry byteorder, dimensions and padding.
cbf_byte_offset.c Implement byte_offset compression and decompression
as designed by A. Hammersley and modified by W. Kabsch.
cbf_canonical.c Fix warnings from gcc 4 on punned pointers. Update
cbf_compress_canonical, cbf_decompress_canonical to
carry byteorder, dimensions and padding.
cbf_codes.c Add support forr base 32K encoding: cbf_tobase32k,
cbf_encode32k_bit_op, cbf_isBigEndian, cbf_endianFix,
cbf_frombase32k, cbf_decode32k_bit_op.
cbf_compress.c Update cbf_compress, cbf_decompress carry byteorder,
dimensions and padding.
cbf_file.c Fix warnings from gcc 4 on punned pointers.
cbf_lex.c Add support for byteorder, dimensions and padding and
base 32K encoding.
cbf_packed.c Update cbf_compress_packed, cbf_decompress_packed to
carry byteorder, dimensions and padding. Add support
for J. P. Abrahams packed compression, versions 1 and
2, while preserving support for original CBFlib flat
packed compression. Add support for 64 bit elements.
cbf_predictor.c Update cbf_compress_predictor,
cbf_decompress_predictor to carry byteorder, dimensions
and padding.
cbf_simple.c Change logic of most image handling routines to work
as special cases of 3d routines. Add new routines
cbf_get_detector_id, cbf_get_real_map_segment,
cbf_get_real_map_segment_mask, cbf_set_map_segment,
cbf_set_map_segment_mask, cbf_set_real_map_segment,
cbf_set_real_map_segment_mask, cbf_get_3d_array_size,
cbf_get_3d_array, cbf_set_3d_array,
cbf_get_axis_reference_setting,
cbf_set_axis_reference_setting,
cbf_construct_reference_detector,
cbf_require_reference_detector,
cbf_set_reference_beam_center.
cbf_read_mime.c Update cbf_parse_mimeheader to read MIME headers for
new compression types and flags and byteorder,
dimensions and padding. Add support for base 32K
encoding.
cbf_tree.c Fix warnings from gcc 4 on punned pointers.
cbf_uncompressed.c Fix handling of 64-bit reads and writes.
cbf_write_binary.c Add code to write out base-32K encoded sections, to
write byte order, dimensions and padding. Add code to
write out MIME headers for packed compressions or
packed version 2 compression with flags for
uncorrelated sections and for flat packed images.
----------------------------------------------------------------------
Release 0.7.6, Herbert J. Bernstein, 15 July 2006
Source File Change
cbf.h Add include of stdio.h; change CBF_LINELENGTH into
CBF_LINELENGTH_10 and CBF_LINELENGTH_11; add new symbols
CBF_CASE_INSENSITIVE, CBF_CASE_SENSITIVE, CBF_LOGERROR,
CBF_LOGWARNING, CBF_LOGWOLINE, CBF_LOGWOCOLUMN,
CBF_LOGSTARTLOC, CBF_LOGCURRENTLOC; add information on
input file and log file to cbf handle struct; and
prototypes for cbf_read_widefile, cbf_write_local_file,
cbf_write_widefile, cbf_column_number,
cbf_blockitem_number, cbf_warning, cbf_error, cbf_log,
cbf_increment_column, cbf_reset_column,
cbf_reset_refcounts, cbf_validate; added valuerow argument
to cbf_set_hashedvalue and caseinsensitive to
cbf_find_hashedvalue.
cbf.c In cbf_make_handle, added include of cbf_ascii.h,
initialized handle->logfile, handle->warnings,
handle->errors, handle->startline, handle->startcolumn;
added new routine cbf_set_logfile; in cbf_free_handle
removed gcc4 warning; broke up cbf_read_file into
cbf_read_anyfile, cbf_read_file, added two more entries to
parse array, one for the cbf handle and one to carry an
auxillary node, such as a parent category; in
cbf_write_file, reset reference counts; added new routine
cbf_write_local_file to allow writing of a local portion
of a cbf instead of the whole thing; added new routines
cbf_column_number and cbf_blockitem_number; added new
routine cbf_log to report parse errors with line numbers;
fixed cbf_require_category when dealing with null
datablocks; fixed cbf_require_column to preserve current
row number; fixed inverted logic in
cbf_require_dictionary; rewrote cbf_set_hashed_value to
deal with insertions correctly; revised
cbf_find_hashedvalue to survive commong errors; revised
cbf_convert_dictionary_definition to recover category
information properly and top deal with more complex
loop-singleton interactions; added new routines
cbf_increment_column, cbf_reset_column,
cbf_reset_refcounts; updated cbf_convert_dictionary to
align database with changes in
cbf_convert_dictionary_definition and to distribute
unspecified items from parents to children; fixed
cbf_find_local_tag for DDL1 names and categories; updated
cbf_find_category_root and cbf_require_category_root to
allow for DDL1 categories drawn from dictionaries; changed
cbf_find_tag_root and cbf_set_tag_root to use
cbf_find_hashedvalue and cbf_set_hashedvalue; added
routines cbf_check_category_tags, cbf_validate.
cbf.stx.y To facilitate validation, changed save frame logic to
append partial save frame to the base cif from the
beginning instead of waiting for the end of the save
frame; added cbf_validate calls at all levels and provided
detailed parse form common errors with reports via cbf_log
cbf_ascii.h Add prototype for cbf_foldtextline.
cbf_ascii.c Added new routine cbf_foldtextline; in cbf_write_ascii
changed logic to no longer backslash-quote individual
embedded semicolons in text fields and to use full
line-folding spec;
cbf_canonical.c fixed gcc4 warning.
cbf_cantext.c fixed gcc4 warnings.
cbf_file.h Add columnlimit to strcut; add prototype for
cbf_make_widefile.
cbf_file.c In cbf_make_file added intialization of line length;
added new routine cbf_make_widefile; in cbf_read_character
do not increment column number at EOF; in cbf_read_line
report lines over the limit
cbf_lex.c Added lexical validation for line length, illegal
characters, long data block names, long save frame names,
failure to provide whitespace after loop_, unterminated
quoted strings.
cbf_packed.c Fix gcc4 warnings
cbf_read_mime.c Pick up corrections to parse of types from work by GD
for X-BASE32K.
cbf_simple.h Add prototypes for cbf_get_bin_sizes, cbf_set_bin_sizes
cbf_simple.c Changed cbf_read_template to use cbf_read_widefile;
added new routines cbf_get_bin_sizes and
cbf_set_bin_sizes; changed cbf_set_gain, cbf_set_overload,
cbf_set_integration_time, cbf_set_datestamp,
cbf_set_axis_setting to force in intervening categories
and columns; in cbf_free_positioner, cbf_free_detector,
fixed gcc4 warnings; revised cbf_set_beam_center to adjust
the displacement rather than the offset.
cbf_tree.h Add symbol for CBF_VALUE as a node type to use for
validation; add prototype for cbf_find_last_typed_child.
cbf_tree.c In cbf_free_node fixed gcc4 warning; added new routine
cbf_find_last_typed_child; changed cbf_make_child to use
cbf_find_last_typed_child instead of cbf_fid_last_child to
avoid confusion between categories and save frames when
the same name is used for both; changed
cbf_compute_hashcode to return values between 0 and 255.
cbf_write.d Add prototype for cbf_compose_itemname.
cbf_write.c In cbf_set_value fold text fields that contain the text
field terminator; add new routine cbf_compose_itemname,
int cbf_write_itemname catch names that are too long;
cif2cbf.c Add "-v dictionary" command line argument and suppress
output to /dev/null and "-w" to process a wide file; add
hooks (based on symbol GNUGETOPT) to use a local copy of
getopt; add text for error exits; add code to load layered
dictionaries.
convert_image.c Add text for error exits; add logic for binning; alias
support with command line arguments "-c
category_alias=category_root" and "-t tag_alias=tag_root",
change from _diffrn_detector.sample_detector_distance to
_diffrn_measurement.sample_detector_distance; change to
support row-major images to agree with adxv; remove most
advisory messages to stdout.
img.h Added rowmajor to struct; redefined img_pixel to be
conditional on rowmajor; added img_pixelptr to get the
pointers to the image.
img.c Added recognition of ADSC QUANTUM315; added row major
support
img2cif.c Changed to use to new img.h macros
makecbf.c Changed to use to new img.h macros
----------------------------------------------------------------------
Release 0.7.5, Herbert J. Bernstein, 15 April 2006
Source File Change
cbf.c Revised header for open source licenses; added
support for aliases, dictionaries and real arrays;
added convenience routines to do searches with default
creation of what is being searched for; added reference
count and dictionary link for cbf handles; added
cbf_new_saveframe, cbf_force_new_saveframe,
cbf_set_saveframename, cbf_reset_saveframe,
cbf_remove_saveframe, cbf_rewind_saveframe,
cbf_rewind_blockitem, cbf_next_saveframe,
cbf_next_blockitem, cbf_select_saveframe,
cbf_select_blockitem, cbf_find_saveframe,
cbf_require_row, cbf_require_nextrow,
cbf_count_saveframes, cbf_count_blockitems,
cbf_saveframe_name, cbf_require_value,
cbf_require_integervalue, cbf_require_doublevalue,
cbf_get_realarrayparameters, cbf_get_realarray,
cbf_set_realarray, cbf_require_datablock,
cbf_require_category, cbf_require_column,
cbf_require_column_value,
cbf_require_column_integervalue,
cbf_require_column_doublevalue,
cbf_get_local_integer_byte_order,
cbf_get_local_real_byte_order,
cbf_get_local_real_format, cbf_get_dictionary,
cbf_set_dictionary, cbf_require_dictionary,
cbf_set_hashedvalue, cbf_find_hashedvalue,
cbf_convert_dictionary_definition,
cbf_convert_dictionary, cbf_find_tag,
cbf_find_local_tag, cbf_srch_tag,
cbf_find_category_root, cbf_require_category_root,
cbf_set_category_root, cbf_find_tag_root,
cbf_require_tag_root, cbf_set_tag_root,
cbf_find_tag_category, cbf_set_tag_category.
cbf.h Revised header for open source licenses; added
definitions of CBF_API_VERSION and CBF_DIC_VERSION;
changed the debug versions of cbf_failnez and
cbf_onfailnez to stringfy the argument; added
dictionary and reference count to cbf_handle
definition; added prototypes for cbf_new_saveframe,
cbf_force_new_saveframe, cbf_set_saveframename,
cbf_remove_saveframe, cbf_rewind_saveframe,
cbf_rewind_blockitem, cbf_next_saveframe,
cbf_next_blockitem, cbf_saveframe_name,
cbf_select_saveframe, cbf_select_blockitem,
cbf_find_saveframe, cbf_require_row,
cbf_require_nextrow, cbf_count_saveframes,
cbf_count_blockitems, cbf_require_value,
cbf_require_integervalue, cbf_require_doublevalue,
cbf_get_realarrayparameters, cbf_get_realarray,
cbf_set_realarray, cbf_require_datablock,
cbf_require_category, cbf_require_column,
cbf_require_column_value,
cbf_require_column_integervalue,
cbf_require_column_doublevalue,
cbf_get_local_integer_byte_order,
cbf_get_local_real_byte_order,
cbf_get_local_real_format, cbf_get_dictionary,
cbf_set_dictionary, cbf_require_dictionary,
cbf_set_hashedvalue, cbf_find_hashedvalue,
cbf_convert_dictionary_definition,
cbf_convert_dictionary, cbf_find_tag,
cbf_find_local_tag, cbf_srch_tag,
cbf_find_category_root, cbf_require_category_root,
cbf_set_category_root, cbf_find_tag_root,
cbf_require_tag_root, cbf_set_tag_root,
cbf_find_tag_category, cbf_set_tag_category,
cbf_alloc.c Revised header for open source licenses.
cbf_alloc.h Revised header for open source licenses.
cbf_ascii.c Revised header for open source licenses.
cbf_ascii.h Revised header for open source licenses.
cbf_binary.c Revised header for open source licenses; added
support of real arrays.
cbf_binary.h Revised header for open source licenses; added
support of real arrays.
cbf_byte_offset.c Revised header for open source licenses; changed
signature for support of real arrays; no actual changes
to the code.
cbf_byte_offset.h Revised header for open source licenses; changed
signature for support of real arrays; no actual changes
to the code.
cbf_canonical.c Revised header for open source licenses; changed
signatures for support of real arrays; no actual
changes to the code.
cbf_canonical.h Revised header for open source licenses; changed
signatures for support of real arrays; no actual
changes to the code.
cbf_codes.c Revised header for open source licenses.
cbf_codes.h Revised header for open source licenses.
cbf_compress.c Revised header for open source licenses; added
support of real arrays.
cbf_compress.h Revised header for open source licenses; added
support of real arrays.
cbf_context.c Revised header for open source licenses.
cbf_context.h Revised header for open source licenses.
cbf_file.c Revised header for open source licenses; added
support of real arrays, making extensive changes to the
handling of integers to get past 32 bit limits.
cbf_file.h Revised header for open source licenses..
cbf_lex.c Revised header for open source licenses; added save
frame support; required whitespace before a comment;
changed WORD to CBFWORD; corrected quoted string parse
to allow for a blank immediately after the opening
quote mark.
cbf_lex.h Revised header for open source licenses.
cbf_packed.c Revised header for open source licenses; changed
signatures for support of real arrays; no actual
changes to the code.
cbf_packed.h Revised header for open source licenses; changed
signatures for support of real arrays; no actual
changes to the code.
cbf_predictor.c Revised header for open source licenses; changed
signatures for support of real arrays; no actual
changes to the code.
cbf_predictor.h Revised header for open source licenses; changed
signatures for support of real arrays; no actual
changes to the code.
cbf_read_binary.c Revised header for open source licenses.
cbf_read_binary.h Revised header for open source licenses.
cbf_read_mime.c Revised header for open source licenses; added
support for real arrays.
cbf_read_mime.h Revised header for open source licenses; added
support for real arrays.
cbf_simple.c Revised header for open source licenses; increased
precision of all numbers to 15 digits; added support
for cells and orientation matrices; built in support
for diffrn_frame_data as an alternative to
diffrn_data_frame; added new routines
cbf_require_diffrn_id, cbf_get_pixel_size,
cbf_set_pixel_size, cbf_get_real_image,
cbf_set_real_image, int cbf_require_detector,
cbf_set_beam_center, cbf_get_inferred_pixel_size,
cbf_get_unit_cell, cbf_set_unit_cell,
cbf_get_reciprocal_cell, cbf_set_reciprocal_cell,
cbf_compute_cell_volume, cbf_compute_reciprocal_cell,
cbf_get_orientation_matrix, cbf_set_orientation_matrix;
added braces to deal with compiler warnings on dangling
else.
cbf_simple.h Revised header for open source licenses; added
prototypes for cbf_require_diffrn_id, cbf_get_array_id,
cbf_get_pixel_size, cbf_set_pixel_size,
cbf_get_real_image, cbf_set_real_image,
cbf_require_detector, cbf_set_beam_center,
cbf_get_inferred_pixel_size, cbf_get_unit_cell,
cbf_set_unit_cell, cbf_get_reciprocal_cell,
cbf_set_reciprocal_cell, cbf_compute_cell_volume,
cbf_compute_reciprocal_cell,
cbf_get_orientation_matrix, cbf_set_orientation_matrix.
cbf_string.c Revised header for open source licenses.
cbf_string.h Revised header for open source licenses.
cbf_stx.c Rebuilt from new cbf.stx.y.
cbf_stx.h Changed WORD to CBFWORD; added SAVE and SAVEEND.
cbf.stx.y Revised header for open source licenses; Revised
grammar to support save frames and to be more
comprehensible; changed name from cbf.stx
cbf_tree.c Revised header for open source licenses; added code
to support save frames, allowing typed searches for
children; added new routines cbf_find_typed_child,
cbf_count_typed_children, cbf_compute_hashcode.
cbf_tree.c Revised header for open source licenses; added
definition of CBF_SAVEFRAME as node type; added
prototypes for cbf_find_typed_child,
cbf_count_typed_children, cbf_compute_hashcode.
cbf.uncompressed.c Revised header for open source licenses; Added
support for real arrays, and to remove 32 bit limits.
cbf.uncompressed.h Revised header for open source licenses; Added
support for real arrays.
cbf.write.c Revised header for open source licenses; added
support for save frames and aliases; changed logic for
single row categories to present item-by-item, instead
of as a loop except for vectors and matrices, present
matrices row by row; carried cbf handle through nest of
calls.
cbf.write.h Revised header for open source licenses; adjusted
prototype of cbf_write_node to carry the cbf handle as
the first argument.
cbf.write_binary.c Revised header for open source licenses; added
support for real arrays.
cbf.write_binary.h Revised header for open source licenses.
Makefile Revised header for open source licenses; defined C++;
added symbol RANLIB for use on systems that require a
ranlib pass after creating a library with ar; added
build and tests of testcell and cif2c; added ADSC test
case to tests of convert_image; updated list of
contents of tar;changed cbf.stx to cbf.stx.y.
connvert_image.c Revised header for open source licenses; added
command line arguments for detector name, detector
distance, rotation and reflection of the image; added
usage report on errors; added code for axis transforms;
added code to report image header fields; cleaned up
PHI reporting; recovered pixel size and beam center
from header; commented out most debug code.
cif2cbf.c Revised header for open source licenses; renamed
BUFSIZ as C2CBUFSIZ to remove a compiler warning;
process save frames.
img2cif.c Revised header for open source licenses; renamed
BUFSIZ as I2CBUFSIZ to remove a compiler warning.
testcell.C New program to test cell functions.
cif2c.c New program to test cell functions.
----------------------------------------------------------------------
Release 0.7.4, Herbert J. Bernstein, 12 January 2004
Source File Change
cbf.c added cbf_set_typeofvalue, cbf_get_typeofvalue; added
braces for nested if-else to remove a compiler warning.
cbf_ascii.c added braces to remove a compiler warnings.
cbf_binary.c added braces to remove a compiler warnings.
cbf_canonical.c added braces to remove a compiler warnings.
cbf_compress.c added braces to remove a compiler warnings.
cbf_file.c simplied dynamic array logic and went to straight
doubling; added braces to remove a compiler warnings.
cbf_lex.c changed parse of quoted strings to allow for embedded
quote marks; removed unused variables; fixed mismatch
of formats; added braces to remove a compiler warnings.
cbf_packed.c added braces to remove a compiler warnings;
intialized variables.
cbf_simple.c typed default typed variable; removed unused
variables; added braces to remove a compiler warnings;
intialized variables.
cbf_uncompressed.c added braces to remove a compiler warnings.
cbf_write.c added internal functions cbf_get_value_type and
cbf_set_value_type for typeofvalue functions; updated
magic number and set magic number to match dictionary,
not CBFlib version; initialized variable.
cbf.h added new external typeofvalue function prototypes;
added notices.
cbf_write.h added new value_type function prototypes.
cif2cbf.c added code to transfer typeofvalue from input to
output to fix handling of nulls; increased buffer to
8192 and called it BUFSIZ; changed from tmpnam to
mkstemp to remove warning; unlinked temporary file;
added braces to remove compiler warnings.
img2cif.c added code to transfer typeofvalue from input to
output to fix handling of nulls; increased buffer to
8192 and called it BUFSIZ; changed from tmpnam to
mkstemp to remove warning; unlinked temporary file;
removed unused variables.
----------------------------------------------------------------------
Release 0.7.3, Paul J. Ellis, 2 October 2002
Source File Change
cbf_simple.c modified cbf_get_image to reorder the image data on read so
that the indices are always increasing in memory (this
behavior was undefined previously).
Note: Early versions of Release 0.7.3 carried the version number 0.7.2.3.
Other than the change in number on 7 Nov 2002, there is no difference
between these versions.
----------------------------------------------------------------------
Release 0.7.2.1, Paul J. Ellis, 7 May 2001
Source File Change
cbf_simple.c corrected nesting in if statements introduced for the prior
mod.
----------------------------------------------------------------------
Release 0.7.2, Herbert J. Bernstein, 22 April 2001
Source File Change
cbf_simple.c changed _diffrn_measurement_axis.id (now deprecated) to
_diffrn_measurement_axis.measurement_id and
_diffrn_detector_axis.id (now deprecated) to
_diffrn_detector_axis.detector_id, but allowed old forms as
aliases.
----------------------------------------------------------------------
Release 0.7.1, Paul J. Ellis, 30 March 2001
Source File Change
cbf_simple.c add reserved argument to various routines; in
cbf_update_pixel use index2 instead of index1; add new
routine cbf_get_pixel_normal; in cbf_get_pixel_area, shift by
(-0.5,-0.5)
----------------------------------------------------------------------
Release 0.7.1, Paul J. Ellis, 13 March 2001
Source File Change
cbf.c remove unused declaration of little.
cbf.h add definitions of CBF_UNDEFINED and
CBF_NOTIMPLEMENTED.
cbf_binary.c cast type argument to (char) in cbf_copy-string call.
cbf_compress.c remove unused declaration of compression_file.
cbf_simple.c add this new routine for higher level calls.
cbf_simple.h add this new header for higher level calls.
cbf_uncompressed.c remove unused declaration of bit.
----------------------------------------------------------------------
Release 0.6.1, H. Powell (per Herbert J. Bernstein), 23 February 2001
Source File Change
cbf.c fix memory leak as corrected by H. Powell
----------------------------------------------------------------------
Release 0.6, Herbert J. Bernstein, 13 January 1999
Source File Change
cbf.c remove argument repeat from cbf_set_integerarray
cbf.h remove argument repeat from cbf_set_integerarray
cbf_binary.h carry compression id in text as argument to
cbf_get/set_bintext, remove repeat as argument to
cbf_set_binary
cbf_binary.c carry compression id in text, rather than header, as
an argument to cbf_get/set_bintext, remove repeat as
argument to cbf_set_binary
cbf_byte_offset.h remove argument repeat from cbf_compress_byte_offset
cbf_byte_offset.c remove argument repeat from cbf_compress_byte_offset
cbf_canonical. remove argument repeat from cbf_compress_canonical
cbf_canonical.c remove argument repeat from cbf_compress_canonical
cbf_compress.h remove argument repeat from cbf_compress, change
argument compression from pointer to value in
cbf_decompress_parameters
cbf_compress.c remove argument repeat from cbf_compress, use
compression as an input argument in
cbf_decompress_parameters, do not write compression id
cbf_file.c tune buffer size allocations to current size
cbf_lex.c carry compression in text, not header, suppress
binary header when there is a MIME header
cbf_packed.h remove argument repeat from cbf_compress_packed
cbf_packed.c remove argument repeat from cbf_compress_packed
cbf_predictor.h remove argument repeat from cbf_compress_predictor
cbf_predictor.c remove argument repeat from cbf_compress_predictor
cbf_read_binary.h make pointer to compression an argument to
cbf_parse_binaryheader
cbf_read_binary.c carry compression in text, not header, suppress
binary header when there is a MIME header
cbf_read_mime.h add prototype for cbf_nblen
cbf_read_mime.c carry compression in text, not header, suppress
binary header when there is a MIME header, allow
trailing blanks on header lines, test for early
terminations, allow arbitrary spacing on element type,
add cbf_nblen
cbf_stx.c rebuilt from cbf.stx with bison 1.25
cbf_tree.c tune allocation of memory for extra children to
current use levels
cbf_uncompressed.h remove argument repeat from cbf_compress_none
cbf_uncompressed.c remove argument repeat from cbf_compress_none
cbf_write.c update version numbers in file headers
cbf_write_binary.c carry compression in text, not header, suppress
binary header when there is a MIME header, quote
X-Binary-Element-Type
----------------------------------------------------------------------
Release 0.5, Paul J. Ellis, 5 December 1998
Source File Change
cbf.c Add option for immediate digest evaluation
(MSG_DIGESTNOW) or deferred digest evaluation
(MSG_DIGEST); adjust layout of error messages; remove
unused repeat.
cbf.stx Add new argument for cbf_set_columnrow.
cbf_ascii.c Add buffer flush.
cbf_binary.c Add call to cbf_codes.h; convert to use of
cbf_get/set_bintext; digests saved in the text for
deferred evaluation.
cbf_byte_offset.c Add storedbits argument on compression; remove repeat
on decompression.
cbf_canonical.c Stylistic cleanup; add storedbits argument on
compression; remove repeat on decompression.
cbf_codes.c Add routines cbf_is_base64digest, cbf_md5digest_to64,
flush buffers when done, general cleanup
cbf_compress.c Add argument bits to cbf_compress and each actual
compression routine, add bits and remove repeat on
decompression.
cbf_file.c Reorganize digest logic; remove nblen argument from
cbf_read_line.
cbf_lex.c Argument type and stylisic cleanup; allow for
deferred digest evaluation, adjust binary size to agree
with MIME size.
cbf_packed.c Stylistic cleanup; add storedbits argument on
compression; remove repeat on decompression.
cbf_predictor.c Add storedbits argument on compression; remove repeat
on decompression.
cbf_read_mime.c Add binary element type logic; cleanup header scan;
allow for deferred digest evaluation.
cbf_tree.c Add argument free to cbf_set_columnrow. If free is
true, free the old value, otherwise a user
responsibility.
cbf_uncompressed.c Add storedbits argument on compression; remove repeat
on decompression.
cbf_write.c Add buffer flush.
cbf_write_binary.c Reorganize digest calculation, adjust binary size by
8, add X-Binary-E;ement-Type.
global.h Change definition of UINT4 from unsigned long int to
unsigned int.
md5.c Mask 32 bits for longer words.
----------------------------------------------------------------------
Release 0.4, Herbert J. Bernstein, 15 November 1998
Source File Change
cbf_stx.c rebuilt from cbf.stx with bison 1.25
cbf_binary.c add digest, elsize, elsign to text
cbf_canonical.c remove write of compression id
cbf_codes.h add argument *digest to cbf_fromqp, cbf_frombase64,
cbf_frombasex
cbf_codes.c add mpack notice, add cbf_md5context_to64, add digest
to cbf_from...
cbf_compress.h add argument *digest to cbf_compress
cbf_compress.c add digest to cbf_compress
cbf_file.h add nscolumn, digest_buffer, digest_bpoint, context
to cbf_file struct, add argument *nblen to
cbf_read_line
cbf_file.c add file->nscolumn, file->digest_buffer,
file->digest_bpoint, update digest when writing
cbf_lex.c add notices, compute digests on intial read
cbf_packed.c do not write compression id
cbf_read_mime.h add prototype for cbf_skip_whitespace, add argument
*compression to cbf_parse_mimeheader
cbf_read_mime.c add notices, remove redundant digest calculation,
adjust handling of compression id, add
cbf_skip_whitespace, have cbf_parse_mimeheader return
compression id, add checks for garbled files, allow
more general headers
cbf_uncompressed.c make uncompressed section free of headers
cbf_write.c update version in headers
cbf_write_binary.c carry digest, elsize, elsign in text rather than
header
----------------------------------------------------------------------
Release 0.3.1.1, Paul J. Ellis, 21 September 1998
Source File Change
cbf.h remove globals, add tolen CBF_TOKEN_MIME_BIN, change
MIME_NOHEADERS to PLAIN_HEADERS, add HDR_DEFAULT, add
arguments ciforcbf, headers, encoding to
cbf_write_file, add argument headers to cbf_read_file,
restore const in several places, merge int
cbf_get_integerarrayparams into
cbf_get_integerarrayparameters
cbf.c add notices, add argument headers to cbf_read_file
to replace use of globals in release 0.2, add arguments
ciforcbf, headers, encoding to cbf_write_file to
replace use of globals in release 0.2, restore some
uses of const, remove integerarrayparams and merge
arguments into cbf_get_integerparameters, replace
cbf_binary_params with cbf_binary_parameters with
extended argument list
cbf.stx add notices, remove gcc use of malloc, define
alloca(x) as NULL, and set large inital depth, adopts
mods from cbf.stx.y in release 0.2
cbf_alloc.c add notices
cbf_ascii.c change use of range of token values to explicit
symbolic tokens
cbf_binary.h merge cbf_binary_params into cbf_binary_parameters,
remove cbf_write_binary
cbf_binary.c add cbf_read_mime.h, and CBF_TOKEN_MIME_BIN token,
use cbf_set/get_fileposition, merge cbf_binary_params
into cbf_binary_parameters, restore some uses of const,
use cbf_decompress_parameters with extended argument
list, use cbf_mime_temp, move cbf_write_binary to its
own file.
cbf_canonical.h add argument binsize to cbf_compress_canonical, add
argument repeat to cbf_decompress_canonical
cbf_canonical.c add notices, remove binbitcount, handle binsize as an
argument
cbf_codes.h new header
cbf_codes.c revise notices, major cleanup.
cbf_compress.c add notices, add compressedsize argument, add repeat
to decompression calls
cbf_context.c add notices
cbf_compress.h add argument compressedsize to cbf_compress, repeat
to cbf_decompress
cbf_file.h map "text..." to "buffer..." in cbf_file, remove
CBFbytedir, change cbf_set_textsize to
cbf_set_buffersize, add cbf_reset_buffer, add
cbf_get_buffer, change cbf_get/put_text to
cbf_get/put_block, add cbf_get/set_position
cbf_file.c add notices, change file->text to file->buffer,
file->text_size to file->buffer_size, file->text_used
to file->buffer_used, file->read_headers,
file->write_headers, file->write_encoding, remove
file->fpos, file->fend, add cbf_get/set_fileposition
cbf_lex.c read by buffers, move MIME processing later in the
flow
cbf_packed.h add compressedsize argument to cbf-compress-packed,
repeat to cbf_decompress_packed, remove ..none,
..byte_off, ..predict
cbf_packed.c add notices, add bitcount argument to cbf_pack_chunk
cbf_predictor.h new header
cbf_predictor.c New routine
cbf_read_binary.h new header
cbf_read_binary.c New routine
cbf_read_mime.h new header
cbf_string.h new header
cbf_string.c New routine, replacing string.c
cbf_stx.c Rebuild of cbf.stx with bison A2.6
cbf_tree.h remove CBF_INDEX, cbf_init_index, cbf_add_index,
cleanup, add const
cbf_tree.c add notices, general cleanup, restore const, remove
cbf_init_index, cbf_add_index
cbf_uncompressed.h new header
cbf_uncompressed.c New routine
cbf_write.c add notices, change tests for "?" and ".", change
range test on tokens to explicit list
cbf_write_binary.h new header
cbf_write_binary.c New routine
global.h new routine with part of md5.h
md5c.c use global.h
md5.h move portion of this header to global.h, from whence
it came
----------------------------------------------------------------------
Release 0.2, Herbert J. Bernstein, 27 August 1998
Source File Change
cbf.h Define CBF and CIF, add cbf_force_new_datablock,
cbf_force_new_category, remove some uses of const, add,
cbf_get_integerarrayparams, add globals CBForCIF,
CIFCRterm, CIFNLterm, CBFbinsize, CBFmime, CBFdigest,
CBFencoding, CBFelsize, CBFbytedir
cbf.c Define CBF and CIF, add cbf_force_new_datablock,
cbf_force_new_category, remove some uses of const, add,
cbf_get_integerarrayparams, add globals CBForCIF,
CIFCRterm, CIFNLterm, CBFbinsize, CBFmime, CBFdigest,
CBFencoding, CBFelsize, CBFbytedir
cbf.stx Add malloc.h when using gcc
cbf.stx.y Version of cbf.stx with changes to allow DDL1
cbf_ascii.c Use symbols for tokens
cbf_binary.h Add cbf_binary_params
cbf_binary.c Add digest logic, change file position tracking
cbf_canonical.c Make writing repeat consistent; track binbitcount add
cbf_binary_params, use cbf_decompress_params; allow MIME
header
cbf_codes.c New routine adapted from mpack
cbf_compress.h Add cbf_decompress_params
cbf_compress.c Add hooks for CBF_NONE, CBF_BYTE_OFFSET, CBF_PREDICTOR,
add cbf_decompress_params
cbf_context.h Remove const from cbf_copy_string
cbf_context.c Remove const from cbf_copy_string
cbf_decode.c New routine adapted from mpack
cbf_file.h Add files to record file position
cbf_file.c Track file position; allow writing CIFs and CBFs
cbf_lex.c Add mime processing; add DDL1 support; process "."
cbf_mime.c New routine
cbf_packed.h Add cbf_compress_none, cbf_decompress_none,
cbf_compress_byte_off, cbf_decompress_byte_off,
cbf_compress_predict, cbf_decompress_predict
cbf_packed.c Add cbf_compress_none, cbf_decompress_none, dummy
cbf_compress_byte_off, dummy cbf_decompress_byte_off,
dummy cbf_compress_predict, dummy cbf_decompress_predict;
ensure consistent writing of repeat
cbf_part.h New header adapted from mpack
cbf_part.c New routine adapted from pack
cbf_stx.c rebuilt with correct bison parser from cbf.stx.y
cbf_tree.c added cbf_make_new_node, cbf_find_last_child,
cbf_name_new_node, cbf_add_new_child, cbf_make_new_child,
cbf_init_index, cbf_add_index; report CBF_ARGUMENT for
cbf_make_child for type CBF_LINK; removed some uses of
const
cbf_write.c Added symbols for parse tokens; recognize "."; adjusted
file header line to conform to documentation; removed some
uses of const
cif2cbf.c New program
common.h New header from mpack
img2cif.c New program
makecbf.c Add local_exit and change cbf_failnez to facilitate
debugging, add _array_intensities.binary_id,
_array_data.binary.id
md5.h New header from mpack
md5c.c New routine from mpack
string.c New routine from mpack
uudecode.c New routine from mpack
----------------------------------------------------------------------
Release 0.1, Paul J. Ellis, 17 April 1998
This was the first CBFlib release. It supported binary CBF files using
binary strings.
----------------------------------------------------------------------
----------------------------------------------------------------------
Updated 13 February 2011. yaya at bernstein-plus-sons dot com
