/********************************************************************** * cbf_canonical.h * * * * Version 0.8.0 20 July 2008 * * * * Paul Ellis and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * * * * (C) Copyright 2006, 2007 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 * * * **********************************************************************/ /*************************** GPL NOTICES ****************************** * * * This program is free software; you can redistribute it and/or * * modify it under the terms of the GNU General Public License as * * published by the Free Software Foundation; either version 2 of * * (the License, or (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program; if not, write to the Free Software * * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA * * 02111-1307 USA * * * **********************************************************************/ /************************* LGPL NOTICES ******************************* * * * This library is free software; you can redistribute it and/or * * modify it under the terms of the GNU Lesser General Public * * License as published by the Free Software Foundation; either * * version 2.1 of the License, or (at your option) any later version. * * * * This library is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * * Lesser General Public License for more details. * * * * You should have received a copy of the GNU Lesser General Public * * License along with this library; if not, write to the Free * * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, * * MA 02110-1301 USA * * * **********************************************************************/ /********************************************************************** * * * Stanford University Notices * * for the CBFlib software package that incorporates SLAC software * * on which copyright is disclaimed * * * * This software * * ------------- * * The term Ôthis softwareÕ, as used in these Notices, refers to * * those portions of the software package CBFlib that were created by * * employees of the Stanford Linear Accelerator Center, Stanford * * University. * * * * Stanford disclaimer of copyright * * -------------------------------- * * Stanford University, owner of the copyright, hereby disclaims its * * copyright and all other rights in this software. Hence, anyone * * may freely use it for any purpose without restriction. * * * * Acknowledgement of sponsorship * * ------------------------------ * * This software was produced by the Stanford Linear Accelerator * * Center, Stanford University, under Contract DE-AC03-76SFO0515 with * * the Department of Energy. * * * * Government disclaimer of liability * * ---------------------------------- * * Neither the United States nor the United States Department of * * Energy, nor any of their employees, makes any warranty, express or * * implied, or assumes any legal liability or responsibility for the * * accuracy, completeness, or usefulness of any data, apparatus, * * product, or process disclosed, or represents that its use would * * not infringe privately owned rights. * * * * Stanford disclaimer of liability * * -------------------------------- * * Stanford University makes no representations or warranties, * * express or implied, nor assumes any liability for the use of this * * software. * * * * Maintenance of notices * * ---------------------- * * In the interest of clarity regarding the origin and status of this * * software, this and all the preceding Stanford University notices * * are to remain affixed to any copy or derivative of this software * * made or distributed by the recipient and are to be affixed to any * * copy of software made or distributed by the recipient that * * contains a copy or derivative of this software. * * * * Based on SLAC Software Notices, Set 4 * * OTT.002a, 2004 FEB 03 * **********************************************************************/ /********************************************************************** * NOTICE * * Creative endeavors depend on the lively exchange of ideas. 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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 * **********************************************************************/ #ifndef CBF_CANONICAL_H #define CBF_CANONICAL_H #ifdef __cplusplus extern "C" { #endif #include #include "cbf_file.h" /* Compression tree node */ typedef struct cbf_compress_nodestruct { size_t count; /* Number in the file */ unsigned int code; /* Code */ unsigned int bitcount; /* Bits in the minimum-redundancy code */ unsigned int bitcode [4]; /* Minimum-redundancy code */ struct cbf_compress_nodestruct *next, *child [2]; } cbf_compress_node; /* Compression data */ typedef struct { cbf_file *file; /* File */ unsigned int bits; /* Coded bits */ unsigned int maxbits; /* Maximum saved bits */ unsigned int endcode; /* End-of-data code endcode = 1 << bits == 2^bits */ size_t nodes; /* Number of nodes */ size_t nextnode; /* Number of nodes used */ cbf_compress_node *node; /* Nodes */ } cbf_compress_data; /* Create compression data */ int cbf_make_compressdata (cbf_compress_data **data, cbf_file *file); /* Free data */ void cbf_free_compressdata (cbf_compress_data *data); /* Initialise compression data arrays */ int cbf_initialise_compressdata (cbf_compress_data *data, unsigned int bits, unsigned int maxbits); /* Write a compression table */ int cbf_put_table (cbf_compress_data *data, unsigned int *bitcount); /* Read a compression table */ int cbf_get_table (cbf_compress_data *data); /* End the bitstream */ int cbf_put_stopcode (cbf_compress_data *data, unsigned int *bitcount); /* Insert a node into a tree */ cbf_compress_node *cbf_insert_node (cbf_compress_node *tree, cbf_compress_node *node); /* Append a node to a list */ cbf_compress_node *cbf_append_node (cbf_compress_node *list, cbf_compress_node *node); /* Convert an ordered tree into an ordered list */ cbf_compress_node *cbf_order_node (cbf_compress_node *tree); /* Create an ordered list */ cbf_compress_node *cbf_create_list (cbf_compress_data *data); /* Combine the two nodes with minimum count */ cbf_compress_node *cbf_reduce_list (cbf_compress_data *data, cbf_compress_node *list); /* Generate the minimum-redundancy code lengths */ int cbf_generate_codelengths (cbf_compress_node *tree, int bitcount); /* Reverse the order of the bits in the bit-codes */ int cbf_reverse_bitcodes (cbf_compress_data *data); /* Generate the canonical bit-codes */ int cbf_generate_canonicalcodes (cbf_compress_data *data); /* Compare the bitcodes of two nodes */ int cbf_compare_bitcodes (const void *void1, const void *void2); /* Construct a tree from an ordered set of nodes */ int cbf_construct_tree (cbf_compress_data *data, cbf_compress_node **node, int bits, cbf_compress_node **root); /* Sort the nodes and set up the decoding arrays */ int cbf_setup_decode (cbf_compress_data *data, cbf_compress_node **start); /* Calculate the expected bit count */ unsigned long cbf_count_bits (cbf_compress_data *data); /* Read a code */ int cbf_get_code (cbf_compress_data *data, cbf_compress_node *root, unsigned int *code, unsigned int *bitcount); /* Write a coded integer */ int cbf_put_code (cbf_compress_data *data, int code, unsigned int overflow, unsigned int *bitcount); /* Count the values */ int cbf_count_values (cbf_compress_data *data, void *source, size_t elsize, int elsign, size_t nelem, int *minelem, int *maxelem, char *border); /* Compress an array */ int cbf_compress_canonical (void *source, size_t elsize, int elsign, size_t nelem, unsigned int compression, cbf_file *file, size_t *compressedsize, int *storedbits, int realarray, const char *byteorder, size_t dimfast, size_t dimmid, size_t dimslow, size_t padding); /* Decompress an array (from the start of the table) */ int cbf_decompress_canonical (void *destination, size_t elsize, int elsign, size_t nelem, size_t *nelem_read, size_t compressedsize, unsigned int compression, int bits, int sign, cbf_file *file, int realarray, const char *byteorder, size_t dimover, size_t dimfast, size_t dimmid, size_t dimslow, size_t padding); #define cbf_decompress_canonical_fs(destination,elsize,elsign,nelem,nelem_read,compressedsize,compression,bits,sign,file,realarray,byteorder,dimover,dimfast,dimmid,dimslow,padding) \ cbf_decompress_canonical((destination),(elsize),(elsign),(nelem),(nelem_read),(compressedsize),(compression),(bits),(sign),(file),(realarray),(byteorder),(dimover),(dimfast),(dimmid),(dimslow),(padding)) #define cbf_decompress_canonical_sf(destination,elsize,elsign,nelem,nelem_read,compressedsize,compression,bits,sign,file,realarray,byteorder,dimover,dimslow,dimmid,dimfast,padding) \ cbf_decompress_canonical((destination),(elsize),(elsign),(nelem),(nelem_read),(compressedsize),(compression),(bits),(sign),(file),(realarray),(byteorder),(dimover),(dimfast),(dimmid),(dimslow),(padding)) #ifdef __cplusplus } #endif #endif /* CBF_CANONICAL_H */