/********************************************************************** * cbf_compress -- compression and decompression * * * * Version 0.7.4 12 January 2004 * * * * Paul Ellis (ellis@ssrl.slac.stanford.edu) and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * **********************************************************************/ /********************************************************************** * NOTICE * * Creative endeavors depend on the lively exchange of ideas. There * * are laws and customs which establish rights and responsibilities * * for authors and the users of what authors create. This notice * * is not intended to prevent you from using the software and * * documents in this package, but to ensure that there are no * * misunderstandings about terms and conditions of such use. * * * * Please read the following notice carefully. If you do not * * understand any portion of this notice, please seek appropriate * * professional legal advice before making use of the software and * * documents included in this software package. In addition to * * whatever other steps you may be obliged to take to respect the * * intellectual property rights of the various parties involved, if * * you do make use of the software and documents in this package, * * please give credit where credit is due by citing this package, * * its authors and the URL or other source from which you obtained * * it, or equivalent primary references in the literature with the * * same authors. * * * * Some of the software and documents included within this software * * package are the intellectual property of various parties, and * * placement in this package does not in any way imply that any * * such rights have in any way been waived or diminished. * * * * With respect to any software or documents for which a copyright * * exists, ALL RIGHTS ARE RESERVED TO THE OWNERS OF SUCH COPYRIGHT. * * * * Even though the authors of the various documents and software * * found here have made a good faith effort to ensure that the * * documents are correct and that the software performs according * * to its documentation, and we would greatly appreciate hearing of * * any problems you may encounter, the programs and documents any * * files created by the programs are provided **AS IS** without any * * warranty as to correctness, merchantability or fitness for any * * particular or general use. * * * * THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF * * PROGRAMS OR DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE * * PROGRAMS OR DOCUMENTS LIES SOLELY WITH THE USERS OF THE PROGRAMS * * OR DOCUMENTS OR FILE OR FILES AND NOT WITH AUTHORS OF THE * * PROGRAMS OR DOCUMENTS. * **********************************************************************/ /********************************************************************** * * * The IUCr Policy * * for the Protection and the Promotion of the STAR File and * * CIF Standards for Exchanging and Archiving Electronic Data * * * * Overview * * * * The Crystallographic Information File (CIF)[1] is a standard for * * information interchange promulgated by the International Union of * * Crystallography (IUCr). CIF (Hall, Allen & Brown, 1991) is the * * recommended method for submitting publications to Acta * * Crystallographica Section C and reports of crystal structure * * determinations to other sections of Acta Crystallographica * * and many other journals. The syntax of a CIF is a subset of the * * more general STAR File[2] format. The CIF and STAR File approaches * * are used increasingly in the structural sciences for data exchange * * and archiving, and are having a significant influence on these * * activities in other fields. * * * * Statement of intent * * * * The IUCr's interest in the STAR File is as a general data * * interchange standard for science, and its interest in the CIF, * * a conformant derivative of the STAR File, is as a concise data * * exchange and archival standard for crystallography and structural * * science. * * * * Protection of the standards * * * * To protect the STAR File and the CIF as standards for * * interchanging and archiving electronic data, the IUCr, on behalf * * of the scientific community, * * * * * holds the copyrights on the standards themselves, * * * * * owns the associated trademarks and service marks, and * * * * * holds a patent on the STAR File. * * * * These intellectual property rights relate solely to the * * interchange formats, not to the data contained therein, nor to * * the software used in the generation, access or manipulation of * * the data. * * * * Promotion of the standards * * * * The sole requirement that the IUCr, in its protective role, * * imposes on software purporting to process STAR File or CIF data * * is that the following conditions be met prior to sale or * * distribution. * * * * * Software claiming to read files written to either the STAR * * File or the CIF standard must be able to extract the pertinent * * data from a file conformant to the STAR File syntax, or the CIF * * syntax, respectively. * * * * * Software claiming to write files in either the STAR File, or * * the CIF, standard must produce files that are conformant to the * * STAR File syntax, or the CIF syntax, respectively. * * * * * Software claiming to read definitions from a specific data * * dictionary approved by the IUCr must be able to extract any * * pertinent definition which is conformant to the dictionary * * definition language (DDL)[3] associated with that dictionary. * * * * The IUCr, through its Committee on CIF Standards, will assist * * any developer to verify that software meets these conformance * * conditions. * * * * Glossary of terms * * * * [1] CIF: is a data file conformant to the file syntax defined * * at http://www.iucr.org/iucr-top/cif/spec/index.html * * * * [2] STAR File: is a data file conformant to the file syntax * * defined at http://www.iucr.org/iucr-top/cif/spec/star/index.html * * * * [3] DDL: is a language used in a data dictionary to define data * * items in terms of "attributes". Dictionaries currently approved * * by the IUCr, and the DDL versions used to construct these * * dictionaries, are listed at * * http://www.iucr.org/iucr-top/cif/spec/ddl/index.html * * * * Last modified: 30 September 2000 * * * * IUCr Policy Copyright (C) 2000 International Union of * * Crystallography * **********************************************************************/ #ifdef __cplusplus extern "C" { #endif #include #include #include #include #include "cbf.h" #include "cbf_alloc.h" #include "cbf_file.h" #include "cbf_compress.h" #include "cbf_canonical.h" #include "cbf_packed.h" #include "cbf_byte_offset.h" #include "cbf_predictor.h" #include "cbf_uncompressed.h" /* Compress an array */ int cbf_compress (void *source, size_t elsize, int elsign, size_t nelem, unsigned int compression, cbf_file *file, size_t *compressedsize, int *bits, char *digest) { int errorcode; size_t size; /* Discard any bits in the buffers */ cbf_failnez (cbf_reset_bits (file)) if (compressedsize) *compressedsize = 0; /* Start a digest? */ if (digest) cbf_failnez (cbf_start_digest (file)) errorcode = 0; size = 0; switch (compression) { case CBF_CANONICAL: errorcode = cbf_compress_canonical (source, elsize, elsign, nelem, compression, file, &size, bits); break; case CBF_PACKED: case 0: errorcode = cbf_compress_packed (source, elsize, elsign, nelem, compression, file, &size, bits); break; case CBF_BYTE_OFFSET: errorcode = cbf_compress_byte_offset (source, elsize, elsign, nelem, compression, file, &size, bits); break; case CBF_PREDICTOR: errorcode = cbf_compress_predictor (source, elsize, elsign, nelem, compression, file, &size, bits); break; case CBF_NONE: errorcode = cbf_compress_none (source, elsize, elsign, nelem, compression, file, &size, bits); break; default: errorcode = CBF_ARGUMENT; } /* Add the compressed size */ if (compressedsize) *compressedsize += size; /* Flush the buffers */ errorcode |= cbf_flush_bits (file); /* Get the digest? */ if (digest) errorcode |= cbf_end_digest (file, digest); /* Done */ return errorcode; } /* Get the parameters of an array (read up to the start of the table) */ int cbf_decompress_parameters (int *eltype, size_t *elsize, int *elsigned, int *elunsigned, size_t *nelem, int *minelem, int *maxelem, unsigned int compression, cbf_file *file) { unsigned int nelem_file; int errorcode, minelement_file, maxelement_file, elsigned_file, elunsigned_file; /* Discard any bits in the buffers */ cbf_failnez (cbf_reset_bits (file)); /* Check compression type */ if (compression != CBF_CANONICAL && compression != CBF_PACKED && compression != CBF_BYTE_OFFSET && compression != CBF_PREDICTOR && compression != CBF_NONE) return CBF_FORMAT; if (compression == CBF_NONE) { nelem_file = 0; minelement_file = maxelement_file = 0; } else { /* Read the number of elements (64 bits) */ cbf_failnez (cbf_get_integer (file, (int *) &nelem_file, 0, 64)) /* Read the minimum element (64 bits) */ errorcode = cbf_get_integer (file, &minelement_file, 1, 64); if (errorcode && errorcode != CBF_OVERFLOW) return errorcode; /* Read the maximum element (64 bits) */ errorcode = cbf_get_integer (file, &maxelement_file, 1, 64); if (errorcode && errorcode != CBF_OVERFLOW) return errorcode; } /* Update the element sign, type, minimum, maximum and number */ elsigned_file = !(((unsigned) minelement_file) <= ((unsigned) maxelement_file) && ((signed) minelement_file) > ((signed) maxelement_file)); elunsigned_file = !(((signed) minelement_file) <= ((signed) maxelement_file) && ((unsigned) minelement_file) > ((unsigned) maxelement_file)); if (elsigned) *elsigned = elsigned_file; if (elunsigned) *elunsigned = elunsigned_file; if (eltype) *eltype = CBF_INTEGER; if (elsize) { /* Calculate the minimum number of bytes needed to hold the elements */ if (minelement_file == 0 && maxelement_file == 0) { *elsize = 0; } else { if ((!elsigned_file || ((signed) minelement_file == (signed short) minelement_file && (signed) maxelement_file == (signed short) maxelement_file)) || (!elunsigned_file || ((unsigned) minelement_file == (unsigned short) minelement_file && (unsigned) maxelement_file == (unsigned short) maxelement_file))) { if ((!elsigned_file || ((signed) minelement_file == (signed char) minelement_file && (signed) maxelement_file == (signed char) maxelement_file)) || (!elunsigned_file || ((unsigned) minelement_file == (unsigned char) minelement_file && (unsigned) maxelement_file == (unsigned char) maxelement_file))) { *elsize = sizeof (char); } else { *elsize = sizeof (short); } } else { *elsize = sizeof (int); } } } if (minelem) *minelem = minelement_file; if (maxelem) *maxelem = maxelement_file; if (nelem) *nelem = nelem_file; /* Success */ return 0; } /* Decompress an array (from the start of the table) */ int cbf_decompress (void *destination, size_t elsize, int elsign, size_t nelem, size_t *nelem_read, unsigned int compression, int bits, int sign, cbf_file *file) { switch (compression) { case CBF_CANONICAL: return cbf_decompress_canonical (destination, elsize, elsign, nelem, nelem_read, compression, file); case CBF_PACKED: case 0: return cbf_decompress_packed (destination, elsize, elsign, nelem, nelem_read, compression, file); case CBF_BYTE_OFFSET: return cbf_decompress_byte_offset (destination, elsize, elsign, nelem, nelem_read, compression, file); case CBF_PREDICTOR: return cbf_decompress_predictor (destination, elsize, elsign, nelem, nelem_read, compression, file); case CBF_NONE: return cbf_decompress_none (destination, elsize, elsign, nelem, nelem_read, compression, bits, sign, file); } /* Fail */ return CBF_ARGUMENT; } #ifdef __cplusplus } #endif