/********************************************************************** * cbf_byte_offset -- byte-offset compression * * * * 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 * **********************************************************************/ #ifdef __cplusplus extern "C" { #endif #include #include #include #include #include #include "cbf.h" #include "cbf_file.h" #include "cbf_byte_offset.h" /* Compress and array with the byte-offset algorithm */ int cbf_compress_byte_offset (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, borrow, element[4], prevelement[4], unsign, sign, limit, bits; unsigned char *unsigned_char_data; unsigned char *unsigned_char_dest=NULL; int delta[4]; int numints, iint, kint; char * border; char * rformat; size_t csize; int bflag=0x800080; int bbflag=0x80000000; int byte0, byte1, byte2, byte3; int sbyte0, sbyte1; unsigned char fixup0; unsigned char fixup1; CBF_UNUSED(dimfast); CBF_UNUSED(dimmid); CBF_UNUSED(dimslow); CBF_UNUSED(padding); CBF_UNUSED(borrow); /* 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; if (bits != 8 && bits != 16 && bits != 32 && 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); } fixup0 = 0x00; fixup1 = 0x80; sbyte0 = byte0 = 0; sbyte1 = byte1 = 1; byte2 = 2; byte3 = 3; if (toupper(border[0]) != toupper(byteorder[0])) { byte0 = 3; byte1 = 2; sbyte0 = byte2 = 1; sbyte1 = byte3 = 0; } if (toupper(byteorder[0]) == 'B'){ fixup0 = 0x80; fixup1 = 0x0; } /* Initialise the pointer */ unsigned_char_data = (unsigned char *) source; /* Set up the previous element for comparison */ prevelement[0] = prevelement[1] = prevelement[2] = prevelement[3] = 0; prevelement[numints-1] = unsign; csize = 0; /* Write the elements */ #ifndef CBF_NOFAST_BYTE_OFFSET /* First try a fast memory-memory transfer */ switch (elsize) { case (1): /* Doing byte_offset with elsize 1 does not make much sense, but we can at least do it quickly */ if (!cbf_set_output_buffersize(file,nelem*2)) { unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used); if (elsign) { char pc = 0; int delta; for (count = 0; count < nelem; count++) { delta = *unsigned_char_data - pc; if (delta < -127 || delta > 127) { *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = delta & 0xff; *unsigned_char_dest++ = (delta >> 8) & 0xff; csize += 3; } else { *unsigned_char_dest++ = delta; csize++; } pc = *unsigned_char_data++; } } else { unsigned char pc = 0; int delta; for (count = 0; count < nelem; count++) { delta = *unsigned_char_data - pc; if (delta < -127 || delta > 127) { *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = delta & 0xff; *unsigned_char_dest++ = (delta >> 8) & 0xff; csize += 3; } else { *unsigned_char_dest++ = delta; csize++; } pc = *unsigned_char_data++; } } file->characters_used+=csize; if (compressedsize) *compressedsize = csize; return 0; } break; case (2): /* We are compressing 16-bit data, which should compress to about half. We allow up to the full size of the original data */ if (!cbf_set_output_buffersize(file,nelem*elsize)) { short int pint; long int dint; short int *sint; if (sizeof(short int) != 2) break; pint = 0; unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used); sint = (short int *) unsigned_char_data; for (count = 0; 3*count < 2*nelem; count++) { dint = (long int)sint[count] - (long int) pint; pint = sint[count]; if (dint <= 127 && dint >= -127) { *unsigned_char_dest++ = (unsigned char)dint; csize ++; } else { if (dint <= 32767 && dint >= -32767) { *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = ((unsigned char *)&dint)[sbyte0]; *unsigned_char_dest++ = ((unsigned char *)&dint)[sbyte1]; csize += 3; } else { *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = fixup0; *unsigned_char_dest++ = fixup1; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte0]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte1]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte2]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte3]; csize +=7; } } } /* At this point nelem-count elements remain and file->characters_size-(csize+file->characters_used) characters remain in the buffer */ if (elsize*(nelem-count) > file->characters_size-(csize+file->characters_used)) { if (compression&CBF_NO_EXPAND) break; if (cbf_set_output_buffersize(file,1024+(nelem*elsize*3)/2)) break; unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used+csize); } for (; count < nelem; count++) { dint = (long int)sint[count] - (long int)pint; pint = sint[count]; if (dint <= 127 && dint >= -127) { *unsigned_char_dest++ = (unsigned char)dint; csize ++; } else { if (dint <= 32767 && dint >= -32767) { if (csize > nelem*elsize-3 ) { if (compression&CBF_NO_EXPAND) return CBF_NOCOMPRESSION; } if (elsize*(nelem-count) > file->characters_size-(csize+file->characters_used)) { if (cbf_set_output_buffersize(file,1024+nelem*elsize*2)) break; unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used+csize); } *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte0]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte1]; csize += 3; } else { if (csize > nelem*elsize-7 ) { if (compression&CBF_NO_EXPAND) return CBF_NOCOMPRESSION; } if (elsize*(nelem-count) > file->characters_size-(csize+file->characters_used)) { if (cbf_set_output_buffersize(file,1024+nelem*elsize*2)) break; unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used+csize); } *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = fixup0; *unsigned_char_dest++ = fixup1; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte0]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte1]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte2]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte3]; csize +=7; } } } file->characters_used+=csize; if (compressedsize) *compressedsize = csize; return 0; } break; case (4): /* We are compressing 32-bit data, which should compress to about one quarter. We allow up to the full size of the original data */ if (!cbf_set_output_buffersize(file,nelem*elsize)) { int pint, dint; short int sint; int *oint; if (sizeof(short int) != 2) break; if (sizeof(int) != 4) break; pint = 0; unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used); oint = (int *) unsigned_char_data; for (count = 0; 7*count < 4*nelem; count++) { dint = oint[count] - pint; pint = oint[count]; if (dint <= 127 && dint >= -127) { *unsigned_char_dest++ = (unsigned char)dint; csize ++; } else if (dint <= 32767 && dint >= -32767) { *unsigned_char_dest++ = 0x80; sint = dint; *unsigned_char_dest++ = ((unsigned char *)&sint)[sbyte0]; *unsigned_char_dest++ = ((unsigned char *)&sint)[sbyte1]; csize += 3; } else { *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = fixup0; *unsigned_char_dest++ = fixup1; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte0]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte1]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte2]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte3]; csize +=7; } } /* At this point nelem-count elements remain and file->characters_size-(csize+file->characters_used) characters remain in the buffer */ if (elsize*(nelem-count) > file->characters_size-(csize+file->characters_used)) { if (compression&CBF_NO_EXPAND) break; if (cbf_set_output_buffersize(file,1024+(nelem*elsize*7)/4)) break; unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used+csize); } for (; count < nelem; count++) { dint = oint[count] - pint; pint = oint[count]; if (dint <= 127 && dint >= -127) { *unsigned_char_dest++ = (unsigned char)dint; csize ++; } else if (dint <= 32767 && dint >= -32767) { *unsigned_char_dest++ = 0x80; sint = dint; *unsigned_char_dest++ = ((unsigned char *)&sint)[sbyte0]; *unsigned_char_dest++ = ((unsigned char *)&sint)[sbyte1]; csize += 3; } else { if (csize > nelem*elsize-7 ) { if (compression&CBF_NO_EXPAND) return CBF_NOCOMPRESSION; } if (elsize*(nelem-count) > file->characters_size-(csize+file->characters_used)) { if (cbf_set_output_buffersize(file,1024+nelem*elsize*2)) break; unsigned_char_dest = (unsigned char *)(file->characters+file->characters_used+csize); } *unsigned_char_dest++ = 0x80; *unsigned_char_dest++ = fixup0; *unsigned_char_dest++ = fixup1; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte0]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte1]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte2]; *unsigned_char_dest++ = ((unsigned char *)&dint)[byte3]; csize +=7; } } file->characters_used+=csize; if (compressedsize) *compressedsize = csize; return 0; } break; default: break; } #endif /* 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; /* Compute the delta */ borrow = 0; kint = 0; if (numints > 1) { for (iint = 0; iint < numints; iint++) delta[iint] = prevelement[iint]; cbf_failnez(cbf_mpint_negate_acc((unsigned int *)delta,numints)); cbf_failnez(cbf_mpint_add_acc((unsigned int *)delta, numints, element, numints)) if (delta[numints-1] & sign) delta[numints-1] |= (~limit); } else { delta[0] = element[0] - prevelement[0]; if (delta[0] & sign) delta[0] |= (~limit); } prevelement[0] = element[0]; for (iint = 1; iint < numints; iint++) { prevelement[iint] = element[iint]; if ((delta[0] >= 0 && delta[iint] != 0 ) || (delta[0] < 0 && (delta[iint]+1)!=0) ) kint = iint; } if (kint == 0) { if (delta[0] <= 127 && delta[0] >= -127) { cbf_failnez(cbf_put_bits(file,&delta[0],8)) csize++; } else if (sizeof(int) > 1 && delta[0] <= 32767 && delta[0] >= -32767) { cbf_failnez(cbf_put_bits(file,&bflag,8)) cbf_failnez (cbf_put_integer (file, delta[0], 1, 16)) csize +=3; } else if ( sizeof(int) > 2 && (sizeof(int) < 5 || ((long)delta[0] <= 2147483647L && (long)delta[0] >= -2147483647L ) ) ){ cbf_failnez(cbf_put_bits(file,&bflag,24)) cbf_failnez(cbf_put_integer (file, delta[0], 1, 32)) csize +=7; } else if (sizeof(int) > 4 ) { cbf_failnez(cbf_put_bits(file,&bflag,24)) cbf_failnez(cbf_put_bits(file,&bbflag,32)) cbf_failnez (cbf_put_integer (file, delta[0], 1, 64)) csize += 15; } else { return CBF_ARGUMENT; } } else { if ((kint+1)*sizeof(int) < 5 ) { cbf_failnez(cbf_put_bits(file,&bflag,24)) for (iint = 0; iint < kint+1; iint++) { cbf_failnez (cbf_put_integer (file, delta[iint], iint==numints-1?1:0, iint<(numints-1)?(CHAR_BIT*sizeof (int)): bits-(CHAR_BIT*sizeof (int))*iint )) } csize += 7; } else if ((kint+1)*sizeof(int) < 9 ) { cbf_failnez(cbf_put_bits(file,&bflag,24)) cbf_failnez(cbf_put_bits(file,&bbflag,32)) for (iint = 0; iint < kint+1; iint++) { cbf_failnez (cbf_put_integer (file, delta[iint], iint==numints-1?1:0, iint<(numints-1)?(CHAR_BIT*sizeof (int)): bits-(CHAR_BIT*sizeof (int))*iint )) } csize += 15; } else return CBF_ARGUMENT; } } /* Return the number of characters written */ if (compressedsize) *compressedsize = csize; /* Success */ return 0; } /* Decompress an array with the byte-offset algorithm */ static int cbf_decompress_byte_offset_slow (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], prevelement[4], sign, unsign, limit; unsigned int data_unsign; unsigned char *unsigned_char_data; int errorcode, overflow, numints, iint, carry; int delta[4]; char * border; char * rformat; size_t numread; CBF_UNUSED(compressedsize); CBF_UNUSED(compression); CBF_UNUSED(byteorder); CBF_UNUSED(dimover); CBF_UNUSED(dimfast); CBF_UNUSED(dimmid); CBF_UNUSED(dimslow); CBF_UNUSED(padding); CBF_UNUSED(carry); CBF_UNUSED(errorcode); /* 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); } /* Set up the previous element for increments */ prevelement[0] = prevelement[1] = prevelement[2] = prevelement[3] = 0; prevelement[numints-1] = data_unsign; /* Read the elements */ overflow = 0; numread = 0; while (numread < nelem) { for (iint=0; iint < numints; iint++){ element[iint] = prevelement[iint]; delta[iint] = 0; } carry = 0; cbf_failnez(cbf_get_bits(file,delta,8)) if ((delta[0]&0xFF) == 0x80) { cbf_failnez(cbf_get_bits(file,delta,16)) if ( (delta[0]& 0xFFFF) == 0x8000) { cbf_failnez(cbf_get_bits(file,delta,32)) if ( (sizeof(int)==2 && delta[0] == 0 && delta[1] == 0x8000) || (sizeof(int)> 3 && (delta[0]&0xFFFFFFFF)==0x80000000) ) { cbf_failnez(cbf_get_bits(file,delta,64)) } else { if (sizeof(int) == 2) { if (delta[1] & 0x8000) { for (iint = 2; iint < numints; iint++) delta[iint] = ~0; } } else { if (delta[0] & 0x80000000) { delta[0] |= ~0xFFFFFFFF; for (iint = 1; iint < numints; iint++) { delta[iint] = ~0; } } } } } else { if (delta[0] & 0x8000) { delta[0] |= ~0xFFFF; for (iint = 1; iint < numints; iint++) { delta[iint] = ~0; } } } } else { if (delta[0]&0x80) { delta[0] |= ~0xFF; for (iint = 1; iint < numints; iint++) { delta[iint] = ~0; } } } if (numints > 1) { for (iint = 0; iint < numints; iint++) element[iint] = prevelement[iint]; cbf_failnez(cbf_mpint_add_acc(element,numints, (unsigned int *)delta,numints)) } else { element[0] = prevelement[0] + delta[0]; element[0] &= limit; } for (iint = 0; iint < numints; iint++) { prevelement[iint] = element[iint]; } /* Make the element signed? */ element[numints-1] -= unsign; #if DEBUGPRINT == 1 fprintf(stderr, "i: %d, 1", numread); fprintf(stderr, " = %d", element[0]); for (iint = 1; iint < numints; iint++) fprintf(stderr, ", %d", element[iint]); fprintf(stderr, "\n"); #endif /* 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; } numread++; } /* Number read */ if (nelem_read) *nelem_read = numread; /* Success */ return overflow; } /* * this fast version assumes chars are 8 bits * and signed integers are represented in two's complement format */ static int cbf_decompress_byte_offset_fast(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 char *unsigned_char_data; char * border; char * rformat; size_t numread; CBF_sll_type delta; int i = 0; unsigned char *rawdata = NULL; CBF_UNUSED(nelem); CBF_UNUSED(compression); CBF_UNUSED(data_sign); CBF_UNUSED(byteorder); CBF_UNUSED(dimover); 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; } if (elsize != 1 && elsize != 2 && elsize != 4 && elsize !=8 ) { 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; /* Initialise the pointer */ unsigned_char_data = (unsigned char *) destination; /* Get the local byte order */ if (realarray) { cbf_get_local_real_byte_order(&border); } else { cbf_get_local_integer_byte_order(&border); } if (file->characters_used < compressedsize) { if (file->temporary) return CBF_FILEREAD; cbf_failnez(cbf_set_io_buffersize(file, compressedsize-(file->characters_used))); if (file->stream == NULL) { fprintf(stderr, "No file stream associated with handle\n"); return CBF_NOTFOUND; } if (fread(file->characters_base+file->characters_used, 1,compressedsize-(file->characters_used), file->stream) != compressedsize-(file->characters_used)) return CBF_FILEREAD; file->characters_used = compressedsize; } rawdata = (unsigned char *)file->characters; numread = 0; if (elsign) { #ifdef CBF_USE_LONG_LONG long long base = 0; unsigned char *baseaddr; if (border[0] == 'b') { baseaddr = (unsigned char *) &base + sizeof(CBF_sll_type) - elsize; } else { baseaddr = (unsigned char *) &base; } #else unsigned int sign, precarry; size_t el0, el1; #if CBF_SLL_INTS == 2 CBF_sll_type base = {0,0}; #else CBF_sll_type base = {0,0,0,0}; size_t el2, el3, fl0, fl1; #endif sign = 1 << (sizeof(unsigned int)*CHAR_BIT-1); if (border[0] == 'b') { #if CBF_SLL_INTS > 2 el0 = 3; el1 = 2; el2 = 1; el3 = 0; fl0 = 1; fl1 = 0; #else el0 = 1; el1 = 0; #endif } else { el0 = 0; el1 = 1; #if CBF_SLL_INTS > 2 el2 = 2; el3 = 3; fl0 = 0; fl1 = 1; #endif } #endif #ifdef CBF_USE_LONG_LONG while (i < compressedsize) { int j; delta = (signed char) rawdata[i++]; if (delta == (signed char) 0x80) { delta = rawdata[i++]; delta |= (signed char) rawdata[i++] << 8; if (delta == (short) 0x8000) { delta = rawdata[i++]; delta |= rawdata[i++] << 8; delta |= rawdata[i++] << 16; delta |= (signed char) rawdata[i++] << 24; if ((long) (delta & 0xffffffff) == (long) 0x80000000) { delta = rawdata[i++]; delta |= rawdata[i++] << 8; delta |= rawdata[i++] << 16; delta |= (unsigned long long) rawdata[i++] << 24; delta |= (unsigned long long) rawdata[i++] << 32; delta |= (unsigned long long) rawdata[i++] << 40; delta |= (unsigned long long) rawdata[i++] << 48; delta |= (signed long long) rawdata[i++] << 56; } } } base += delta; for (j = 0; j < elsize; j++) *unsigned_char_data++ = baseaddr[j]; numread++; } #else #if CBF_SLL_INTS==2 while (i < (int)compressedsize) { delta.el1 = 0; delta.el0 = (signed char) rawdata[i++]; if ((int)delta.el0 == (signed char) 0x80) { delta.el0 = rawdata[i++]; delta.el0 |= (signed char) rawdata[i++] << 8; if (delta.el0 & 0x8000L) { delta.el0 |= ~0x7FFFL; delta.el1 = (unsigned int)~0L; } if ((delta.el0 & 0xffffL) == 0x8000) { delta.el1 = 0; delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el0 |= rawdata[i++] << 16; delta.el0 |= (signed char) rawdata[i++] << 24; if (delta.el0 & 0x80000000L) { delta.el0 |= ~0x7FFFFFFFL; delta.el1 = (unsigned int)~0L; } if ((delta.el0 & 0xffffffffL) == 0x80000000L) { delta.el0 = 0; delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el0 |= rawdata[i++] << 16; delta.el0 |= rawdata[i++] << 24; delta.el1 = rawdata[i++]; delta.el1 |= rawdata[i++] << 8; delta.el1 |= rawdata[i++] << 16; delta.el1 |= (signed char) rawdata[i++] << 24; } } } precarry = 0; if (base.el0 & sign) precarry++; if (delta.el0 & sign) precarry++; base.el0 += delta.el0; if (precarry == 2 || (precarry == 1 && !(base.el0&sign) ) ) base.el1++; base.el1+= delta.el1; switch (elsize) { case (sizeof(unsigned int) *2): ((unsigned int *)unsigned_char_data)[el0] = base.el0; ((unsigned int *)unsigned_char_data)[el1] = base.el1; break; case (sizeof(unsigned int) ): ((unsigned int *)unsigned_char_data)[0] = base.el0; break; case (sizeof(unsigned short) ): ((unsigned short *)unsigned_char_data)[0] = (unsigned short)base.el0; break; case (sizeof(unsigned char) ): ((unsigned char *)unsigned_char_data)[0] = (unsigned char)base.el0; break; } unsigned_char_data+= elsize; numread++; } #else while (i < compressedsize) { delta.el1 = delta.el2 = delta.el3 = 0; delta.el0 = (signed char) rawdata[i++]; if (delta.el0 == (signed char) 0x80) { delta.el0 = rawdata[i++]; delta.el0 |= (signed char) rawdata[i++] << 8; if (delta.el0 & 0x8000) delta.el1 = delta.el2 = delta.el3 = ~0; if ((delta.el0 & 0xffff) == 0x8000) { delta.el2 = delta.el3 = 0; delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el1 = rawdata[i++]; delta.el1 |= (signed char) rawdata[i++] << 8; if (delta.el1 & 0x8000) delta.el2 = delta.el3 = ~0; if (delta.el0 == 0 && (delta.el1 & 0x8000) == 0x8000) { delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el1 = rawdata[i++]; delta.el1 |= rawdata[i++] << 8; delta.el2 = rawdata[i++]; delta.el2 |= rawdata[i++] << 8; delta.el3 = rawdata[i++]; delta.el3 |= (signed char)rawdata[i++] << 8; } } } precarry = 0; if (base.el0 & sign) precarry++; if (delta.el0 & sign) precarry++; base.el0 += delta.el0; if (precarry == 2 || (precarry == 1 && !(base.el0&sign) ) ) base.el1++; precarry = 0; if (base.el1 & sign) precarry++; if (delta.el1 & sign) precarry++; base.el1+= delta.el1; if (precarry == 2 || (precarry == 1 && !(base.el1&sign) ) ) base.el2++; precarry = 0; if (base.el2 & sign) precarry++; if (delta.el2 & sign) precarry++; base.el2+= delta.el2; if (precarry == 2 || (precarry == 1 && !(base.el1&sign) ) ) base.el3++; base.el1+= delta.el1; switch (elsize) { case (sizeof(unsigned int) *4): ((unsigned int *)unsigned_char_data)[el0] = base.el0; ((unsigned int *)unsigned_char_data)[el1] = base.el1; ((unsigned int *)unsigned_char_data)[el2] = base.el2; ((unsigned int *)unsigned_char_data)[el3] = base.el3; break; case (sizeof(unsigned int) *2 ): ((unsigned int *)unsigned_char_data)[fl0] = base.el0; ((unsigned int *)unsigned_char_data)[fl1] = base.el1; break; case (sizeof(unsigned char) ): ((unsigned char *)unsigned_char_data)[0] = base.el0; break; } unsigned_char_data+= elsize; numread++; } #endif #endif } else { #ifdef CBF_USE_LONG_LONG unsigned long long base = 0; unsigned long long basemask = 0; unsigned char *baseaddr; int j; for (j = 0; j < elsize*8; j++) { basemask <<= 1; basemask |= 1; } if (border[0] == 'b') { baseaddr = (unsigned char *) &base + sizeof(CBF_ull_type) - elsize; } else { baseaddr = (unsigned char *) &base; } #else unsigned int sign, precarry; size_t el0, el1; #if CBF_ULL_INTS == 2 CBF_ull_type base = {0,0}; #else CBF_ull_type base = {0,0,0,0}; size_t el2, el3, fl0, fl1; #endif sign = 1 << (sizeof(unsigned int)*CHAR_BIT-1); if (border[0] == 'b') { #if CBF_ULL_INTS > 2 el0 = 3; el1 = 2; el2 = 1; el3 = 0; fl0 = 1; fl1 = 2; #else el0 = 1; el1 = 0; #endif } else { el0 = 0; el1 = 1; #if CBF_SLL_INTS > 2 el2 = 2; el3 = 3; fl0 = 0; fl1 = 1; #endif } #endif #ifdef CBF_USE_LONG_LONG while (i < compressedsize) { delta = (signed char) rawdata[i++]; if (delta == (signed char) 0x80) { delta = rawdata[i++]; delta |= (signed char) rawdata[i++] << 8; if (delta == (short) 0x8000) { delta = rawdata[i++]; delta |= rawdata[i++] << 8; delta |= rawdata[i++] << 16; delta |= (signed char) rawdata[i++] << 24; if ((long) (delta & 0xffffffff) == (long) 0x80000000) { delta = rawdata[i++]; delta |= rawdata[i++] << 8; delta |= rawdata[i++] << 16; delta |= (unsigned long long) rawdata[i++] << 24; delta |= (unsigned long long) rawdata[i++] << 32; delta |= (unsigned long long) rawdata[i++] << 40; delta |= (unsigned long long) rawdata[i++] << 48; delta |= (signed long long) rawdata[i++] << 56; } } } base += delta; base &= basemask; for (j = 0; j < elsize; j++) *unsigned_char_data++ = baseaddr[j]; numread++; } #else #if CBF_SLL_INTS==2 while (i < (int)compressedsize) { delta.el1 = 0; delta.el0 = (signed char) rawdata[i++]; if ((int)delta.el0 == (signed char) 0x80) { delta.el0 = rawdata[i++]; delta.el0 |= (signed char) rawdata[i++] << 8; if (delta.el0 & 0x8000L) { delta.el0 |= ~0x7FFFL; delta.el1 = (unsigned int)~0L; } if ((delta.el0 & 0xffff) == 0x8000) { delta.el1 = 0; delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el0 |= rawdata[i++] << 16; delta.el0 |= (signed char) rawdata[i++] << 24; if (delta.el0 & 0x80000000L) delta.el1 = ~0; if ((delta.el0 & 0xffffffff) == 0x80000000) { delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el0 |= rawdata[i++] << 16; delta.el0 |= rawdata[i++] << 24; delta.el1 = rawdata[i++]; delta.el1 |= rawdata[i++] << 8; delta.el1 |= rawdata[i++] << 16; delta.el1 |= (signed char) rawdata[i++] << 24; } } } precarry = 0; if (base.el0 & sign) precarry++; if (delta.el0 & sign) precarry++; base.el0 += delta.el0; if (precarry == 2 || (precarry == 1 && !(base.el0&sign) ) ) base.el1++; base.el1+= delta.el1; base.el1 &= 0xffffffffL; switch (elsize) { case (sizeof(unsigned int) *2): ((unsigned int *)unsigned_char_data)[el0] = base.el0; ((int *)unsigned_char_data)[el1] = (int)base.el1; break; case (sizeof(int) ): ((int *)unsigned_char_data)[0] = (int)base.el0; break; case (sizeof(short) ): ((short *)unsigned_char_data)[0] = (short)base.el0; break; case (sizeof(char) ): ((char *)unsigned_char_data)[0] = (char)base.el0; break; } unsigned_char_data+= elsize; numread++; } #else while (i < compressedsize) { delta.el1 = delta.el2 = delta.el3 = 0; delta.el0 = (signed char) rawdata[i++]; if (delta.el0 == (signed char) 0x80) { delta.el0 = rawdata[i++]; delta.el0 |= (signed char) rawdata[i++] << 8; if (delta.el0 & 0x8000) delta.el1 = delta.el2 = delta.el3 = ~0; if ((delta.el0&0xffff) == 0x8000) { delta.el2 = delta.el3 = 0; delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el1 = rawdata[i++]; delta.el1 |= (signed char) rawdata[i++] << 8; if (delta.el1 & 0x8000) delta.el2 = delta.el3 = ~0; if (delta.el0 == 0 && (delta.el1&0x8000) == 0x8000) { delta.el0 = rawdata[i++]; delta.el0 |= rawdata[i++] << 8; delta.el1 = rawdata[i++]; delta.el1 |= rawdata[i++] << 8; delta.el2 = rawdata[i++]; delta.el2 |= rawdata[i++] << 8; delta.el3 = rawdata[i++]; delta.el3 |= (signed char)rawdata[i++] << 8; } } } precarry = 0; if (base.el0 & sign) precarry++; if (delta.el0 & sign) precarry++; base.el0 += delta.el0; if (precarry == 2 || (precarry == 1 && !(base.el0&sign) ) ) base.el1++; precarry = 0; if (base.el1 & sign) precarry++; if (delta.el1 & sign) precarry++; base.el1+= delta.el1; if (precarry == 2 || (precarry == 1 && !(base.el1&sign) ) ) base.el2++; precarry = 0; if (base.el2 & sign) precarry++; if (delta.el2 & sign) precarry++; base.el2+= delta.el2; if (precarry == 2 || (precarry == 1 && !(base.el1&sign) ) ) base.el3++; base.el3+= delta.el3; base.el3 &= 0xffff; switch (elsize) { case (sizeof(unsigned int) *4): ((unsigned int *)unsigned_char_data)[el0] = base.el0; ((unsigned int *)unsigned_char_data)[el1] = base.el1; ((unsigned int *)unsigned_char_data)[el2] = base.el2; ((int *)unsigned_char_data)[el3] = base.el3; break; case (sizeof(unsigned int) *2 ): ((unsigned int *)unsigned_char_data)[fl0] = base.el0; ((int *)unsigned_char_data)[fl1] = base.el1; break; case (sizeof( char) ): (( char *)unsigned_char_data)[0] = (char)base.el0; break: } unsigned_char_data+= elsize; numread++; } #endif #endif } /* Number read */ if (nelem_read) *nelem_read = numread; /* Success */ return 0; } int cbf_decompress_byte_offset(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) { /* test for bits left in buffer, element size, chars are 8-bit, and signed integers are represented in two's complement */ if (file->bits[0] != 0 || elsize > sizeof(CBF_ull_type) || CHAR_BIT != 8 || ~0 != -1 || (elsize != 1 && elsize != 2 && elsize != 4 && elsize !=8 ) ) { return cbf_decompress_byte_offset_slow(destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, data_bits, data_sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); } return cbf_decompress_byte_offset_fast(destination, elsize, elsign, nelem, nelem_read, compressedsize, compression, data_bits, data_sign, file, realarray, byteorder, dimover, dimfast, dimmid, dimslow, padding); } #ifdef __cplusplus } #endif