/********************************************************************** * cbf_uncompressed -- uncompressed binary sections * * * * 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. 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 #if !defined(_MSC_VER) #define __USE_XOPEN #define _XOPEN_SOURCE #include #endif #include "cbf.h" #include "cbf_alloc.h" #include "cbf_compress.h" #include "cbf_file.h" #include "cbf_uncompressed.h" #include "cbf_string.h" #define CBF_SHIFT63 (sizeof (int) * CHAR_BIT > 64 ? 63 : 0) /* Copy an array without compression */ int cbf_compress_none (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) { unsigned int count, element[4], unsign, sign, limit, bits; unsigned char *unsigned_char_data; int numints, iint; char * border; char * rformat; CBF_UNUSED( compression ); CBF_UNUSED( dimfast ); CBF_UNUSED( dimmid ); CBF_UNUSED( dimslow ); CBF_UNUSED( padding ); /* Is the element size valid? */ if (elsize != sizeof (int) && elsize != 2* sizeof (int) && elsize != 4* sizeof (int) && elsize != sizeof (short) && elsize != sizeof (char)) return CBF_ARGUMENT; /* check for compatible real format */ if ( realarray ) { cbf_failnez (cbf_get_local_real_format(&rformat) ) if ( strncmp(rformat,"ieee",4) ) return CBF_ARGUMENT; } bits = elsize * CHAR_BIT; if (bits < 1 || bits > 64) return CBF_ARGUMENT; numints = (bits + CHAR_BIT*sizeof (int) -1)/(CHAR_BIT*sizeof (int)); /* Maximum limits */ sign = 1 << ((elsize-(numints-1)*sizeof(int))* CHAR_BIT - 1); if (elsize == sizeof (int) || elsize == numints*sizeof(int) ) limit = ~0; else if (numints == 1) { limit = ~-(1 << (elsize * CHAR_BIT)); } else { limit = ~-(1 << ((elsize-(numints-1)*sizeof(int)) * CHAR_BIT)); } if (storedbits) *storedbits = bits; /* Offset to make the value unsigned */ if (elsign) unsign = sign; else unsign = 0; /* Get the local byte order */ if (realarray) { cbf_get_local_real_byte_order(&border); } else { cbf_get_local_integer_byte_order(&border); } /* Initialise the pointer */ unsigned_char_data = (unsigned char *) source; /* Write the elements */ /* Try for a fast memory-memory transfer */ switch (elsize) { case (1): if (!cbf_set_output_buffersize(file,nelem)) { memmove((void *)(file->characters+file->characters_used), (void *)unsigned_char_data,nelem); file->characters_used+=nelem; if (compressedsize) *compressedsize = nelem; return 0; } break; case (2): case (4): case (8): if (!cbf_set_output_buffersize(file,nelem*elsize)) { if (toupper(border[0]) == toupper(byteorder[0])) { memmove((void *)(file->characters+file->characters_used), (void *)unsigned_char_data,nelem*elsize); } else { if ((elsize == 4 || elsize == 8) && sizeof(short int) !=2 ) break; if (elsize == 8 && sizeof(int) !=4 ) break; cbf_swab((void *)unsigned_char_data, (void *)(file->characters+file->characters_used), nelem*elsize); if (elsize == 4 || elsize == 8) { short int temp; short int *sint; sint = (short int *)(file->characters+file->characters_used); for (count = 0; count < elsize * nelem; count+= 4) { temp = *sint; *sint = sint[1]; sint[1] = temp; sint+=2; } } if (elsize == 8) { int temp; int *oint; oint = (int *)(file->characters+file->characters_used); for (count = 0; count < elsize * nelem; count+= 8) { temp = *oint; *oint = oint[1]; oint[1] = temp; oint+=2; } } } file->characters_used+=nelem*elsize; if (compressedsize) *compressedsize = nelem*elsize; return 0; } break; default: break; } /* If we got here, we will do it the slow, painful way */ for (count = 0; count < nelem; count++) { /* Get the next element */ if (numints > 1) { if (border[0] == 'b') { for (iint = numints; iint; iint--) { element[iint-1] = *((unsigned int *) unsigned_char_data); unsigned_char_data += sizeof (int); } } else { for (iint = 0; iint < numints; iint++) { element[iint] = *((unsigned int *) unsigned_char_data); unsigned_char_data += sizeof (int); } } } else { if (elsize == sizeof (int)) element[0] = *((unsigned int *) unsigned_char_data); else if (elsize == sizeof (short)) element[0] = *((unsigned short *) unsigned_char_data); else element[0] = *unsigned_char_data; unsigned_char_data += elsize; } /* Make the element unsigned */ element[numints-1] += unsign; element[numints-1] &= limit; /* Write the element to the file */ element[numints-1] -= unsign; if (numints > 1) { for (iint = 0; iint < numints; iint++) { cbf_failnez (cbf_put_integer (file, element[iint], 0, iint<(numints-1)?(CHAR_BIT*sizeof (int)): bits-(CHAR_BIT*sizeof (int))*iint )) } } else { cbf_failnez (cbf_put_integer (file, element[0], 0, bits)) } } /* Return the number of characters written */ if (compressedsize) *compressedsize = (nelem * bits + 7) / 8; /* Success */ return 0; } /* Recover an array without decompression */ int cbf_decompress_none (void *destination, size_t elsize, int elsign, size_t nelem, size_t *nelem_read, size_t compressedsize, unsigned int compression, int data_bits, int data_sign, cbf_file *file, int realarray, const char *byteorder, size_t dimover, size_t dimfast, size_t dimmid, size_t dimslow, size_t padding) { unsigned int element[4], sign, unsign, limit, count; unsigned int data_unsign; unsigned char *unsigned_char_data; int errorcode, overflow, numints, iint; char * border; char * rformat; CBF_UNUSED( compressedsize ); CBF_UNUSED( compression ); CBF_UNUSED( byteorder ); CBF_UNUSED( dimover ); CBF_UNUSED( dimfast ); CBF_UNUSED( dimmid ); CBF_UNUSED( dimslow ); CBF_UNUSED( padding ); /* prepare the errorcode */ errorcode = 0; /* Is the element size valid? */ if (elsize != sizeof (int) && elsize != 2* sizeof (int) && elsize != 4* sizeof (int) && elsize != sizeof (short) && elsize != sizeof (char)) return CBF_ARGUMENT; /* check for compatible real format */ if ( realarray ) { cbf_failnez (cbf_get_local_real_format(&rformat) ) if ( strncmp(rformat,"ieee",4) ) return CBF_ARGUMENT; } /* Check the stored element size */ if (data_bits < 1 || data_bits > 64) return CBF_ARGUMENT; numints = (data_bits + CHAR_BIT*sizeof (int) -1)/(CHAR_BIT*sizeof (int)); /* Initialise the pointer */ unsigned_char_data = (unsigned char *) destination; /* Maximum limits */ sign = 1 << ((elsize-(numints-1)*sizeof(int))* CHAR_BIT - 1); if (elsize == sizeof (int) || elsize == numints*sizeof(int)) limit = ~0; else if (numints == 1 ) { limit = ~(-(1 << (elsize * CHAR_BIT))); } else { limit = ~(-(1 << ((elsize-(numints-1)*sizeof(int)) * CHAR_BIT))); } /* Offsets to make the value unsigned */ if (data_sign) data_unsign = sign; else data_unsign = 0; if (elsign) unsign = sign; else unsign = 0; /* Get the local byte order */ if (realarray) { cbf_get_local_real_byte_order(&border); } else { cbf_get_local_integer_byte_order(&border); } /* Read the elements */ count = 0; overflow = 0; while (count < nelem) { /* Get the next element */ if (numints > 1 ) { for (iint=0; iint < numints; iint++) { errorcode |= cbf_get_integer (file, (int *)&(element[iint]), iint<(numints-1)?0:data_sign, iint<(numints-1)?(CHAR_BIT*sizeof (int)): data_bits-(CHAR_BIT*sizeof (int))*iint); } } else { errorcode |= cbf_get_integer (file, (int *)&(element[0]), data_sign, data_bits); } if (errorcode) { if ((errorcode&CBF_OVERFLOW) == CBF_OVERFLOW) overflow = errorcode; else { if (nelem_read) *nelem_read = count; return errorcode | overflow; } } /* Make the element unsigned */ element[numints-1] += data_unsign; element[numints-1] &= limit; /* Make the element signed? */ element[numints-1] -= unsign; /* Save the element */ if (numints > 1) { if (border[0] == 'b') { for (iint = numints; iint; iint--) { *((unsigned int *) unsigned_char_data) = element[iint-1]; unsigned_char_data += sizeof (int); } } else { for (iint = 0; iint < numints; iint++) { *((unsigned int *) unsigned_char_data) = element[iint]; unsigned_char_data += sizeof (int); } } } else { if (elsize == sizeof (int)) *((unsigned int *) unsigned_char_data) = element[0]; else if (elsize == sizeof (short)) *((unsigned short *) unsigned_char_data) = element[0]; else *unsigned_char_data = element[0]; unsigned_char_data += elsize; } count++; } /* Number read */ if (nelem_read) *nelem_read = count; /* Success */ return overflow; } #ifdef __cplusplus } #endif