/********************************************************************** * An optimized byte-offset decompression * * * * Based on CBFlib Version 0.8.0 20 July 2008 * * * * Assumptions: * * elsize: the size of the integer element is 4 bytes * * elsign: is always 1. Means integer element type is signed? * * data_bits: the number of bits in the integer element is 32 * * CHAR_BIT: the number of bits in a byte is 8 * * data_sign: is always 1. Signed integer type for the data? * * realarray: is 0; the type of the data is always integer, not real * * * * (C) Copyright 2009 Nicholas K. Sauter * * * **********************************************************************/ /********************************************************************** * 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 * * * **********************************************************************/ /************************* 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. 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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 #include "cbf.h" extern "C" { #endif #include #include #include #include #include #include "cbf_file.h" #include "cbf_byte_offset.h" #include /* Changes made in the byte-offset algorithm Baseline performance for one cbf decompression 0.26 sec Eliminated all code that tests numints, since it is always==1 0.23 sec Remove dependency on data_bits 0.23 sec Remove dependency on realarray -- it is always 0 0.23 sec Remove cbf_failnez macro resolution overhead 0.23 sec Eliminate function call overhead to cbf_get_bits(*,*,8) 0.18 sec When bitcount==8 also omit variable count==0; while loop once 0.14 sec Remove dependency on elsize--always 4 bytes 0.13 sec Eliminate cases where sizeof(int) != 4 0.13 sec file->characters_used == 0 for bitcount==8 0.13 sec double buffering--substitute fread for getc 0.09 sec */ /* Decompress an array with the byte-offset algorithm */ int cbf_decompress_byte_offset_optimized (void *destination, size_t elsize, int elsign, size_t nelem, size_t *nelem_read, int data_bits, int data_sign, cbf_file *file, int realarray) { unsigned int element[4], prevelement[4], sign, unsign, limit; unsigned int data_unsign; unsigned char *unsigned_char_data; int errorcode, overflow, iint, carry; int delta[4]; char * border; char * rformat; size_t numread; /* home-brewed buffered I/O */ unsigned char dbuf[128]; static int dbuf_size = 128; size_t ifile_still_buffered; long cbf_file_position; /* ported from cbf_get_bits */ int get_bits_bitcode, get_bits_m, get_bits_maxbits, get_bits_bitcount; get_bits_maxbits = sizeof (int) * CHAR_BIT; /* is always 32 */ ifile_still_buffered = 0; /* prepare the errorcode */ errorcode = 0; /* Initialise the pointer */ unsigned_char_data = (unsigned char *) destination; /* Maximum limits */ sign = 1 << (elsize - 1); limit = ~0; /* 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 */ cbf_get_local_integer_byte_order(&border); /* Set up the previous element for increments */ prevelement[0] = prevelement[1] = prevelement[2] = prevelement[3] = 0; prevelement[0] = data_unsign; /* Read the elements */ overflow = 0; numread = 0; while (numread < nelem) { { element[0] = prevelement[0]; delta[0] = 0; } carry = 0; get_bits_bitcount = 8; /* Read the bits into an int */ get_bits_bitcode = file->bits [1] & 0x0ff; /*file->bits [1] = getc (file->stream);*/ if (!ifile_still_buffered) { cbf_file_position = ftell(file->stream); ifile_still_buffered = fread(dbuf, 1, dbuf_size, file->stream); } file->bits[1] = (int)(dbuf[dbuf_size-ifile_still_buffered]); ifile_still_buffered--; cbf_file_position++; if (file->bits [1] == EOF) return CBF_FILEREAD; get_bits_bitcode |= (file->bits [1] << 0) & -(1 << 0); file->bits [1] =(file->bits [1] >> (8 + get_bits_bitcount)); file->bits [0] = 0; /* Sign-extend */ get_bits_m = 1 << (get_bits_bitcount - 1); if (get_bits_bitcode & get_bits_m) *delta = get_bits_bitcode | -get_bits_m; else *delta = get_bits_bitcode & ~-get_bits_m; if ((delta[0]&0xFF) == 0x80) { ifile_still_buffered = 0; fseek(file->stream, cbf_file_position, SEEK_SET); cbf_get_bits(file,delta,16); cbf_file_position = ftell(file->stream); if ( (delta[0]& 0xFFFF) == 0x8000) { ifile_still_buffered = 0; fseek(file->stream, cbf_file_position, SEEK_SET); cbf_get_bits(file,delta,32); cbf_file_position = ftell(file->stream); if ( (delta[0]&0xFFFFFFFF)==0x80000000 ) { ifile_still_buffered = 0; fseek(file->stream, cbf_file_position, SEEK_SET); cbf_get_bits(file,delta,64); cbf_file_position = ftell(file->stream); } else { if (delta[0] & 0x80000000) { delta[0] |= ~0xFFFFFFFF; } } } else { if (delta[0] & 0x80000) { delta[0] |= ~0xFFFF; } } } else { if (delta[0]&0x80) { delta[0] |= ~0xFF; } } element[0] = prevelement[0] + delta[0]; element[0] &= limit; { prevelement[0] = element[0]; } /* Make the element signed? */ element[0] -= unsign; /* Save the element */ *((unsigned int *) unsigned_char_data) = element[0]; unsigned_char_data += elsize; numread++; } /* Number read */ if (nelem_read) *nelem_read = numread; /* Success */ return overflow; } #ifdef __cplusplus } #endif