CBFlib ChangeLog An API for CBF/imgCIF Crystallographic Binary Files with ASCII Support Version 0.7.4 12 January 2004 by Paul J. Ellis Stanford Synchrotron Radiation Laboratory ellis@ssrl.slac.stanford.edu and Herbert J. Bernstein Bernstein + Sons yaya@bernstein-plus-sons.com ------------------------------------------------------------------------ Before using this software, please read the for important disclaimers and the IUCr Policy on the Use of the Crystallographic Information File (CIF) and for other important information. ------------------------------------------------------------------------ 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 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 ------------------------------------------------------------------------ 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 12 January 2004. yaya@bernstein-plus-sons.com