/********************************************************************** * tiffcbf -- convert a tiff file to a cbf file * * * * Version 0.7.6 28 June 2006 * * * * Paul Ellis and * * Herbert J. Bernstein (yaya@bernstein-plus-sons.com) * * * * (C) Copyright 2006 Herbert J. Bernstein * * * **********************************************************************/ /********************************************************************** * * * YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE GPL * * WHILE YOU MAY ALTERNATIVE DISTRIBUTE THE API UNDER THE LGPL * * YOU MAY ***NOT*** DISTRBUTE THIS PROGRAM UNDER 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 * * * **********************************************************************/ /********************************************************************** * 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 * **********************************************************************/ #include "cbf.h" #include #include #include #include #include #include int local_exit(int); int local_exit(int status) { exit(status); return status; /* to avoid warning messages */ } #undef cbf_failnez #define cbf_failnez(x) \ {int err; \ err = (x); \ if (err) { \ fprintf(stderr,"\nCBFlib fatal error %x \n",err); \ local_exit(-1); \ } \ } int main (int argc, char *argv []) { FILE *out; TIFF *tif; cbf_handle cbf; clock_t a,b; uint32 width; uint32 height; uint32 npixels; unsigned char * raster; int imageno; /* Usage */ if (argc < 3) { fprintf (stderr, "\n Usage: %s tifffile cbffile\n", argv [0]); exit (2); } /* Read the tiff image */ a = clock (); if (!(tif=TIFFOpen(argv[1], "r"))) { fprintf(stderr," %s unable to open tiff image %s, abort\n", argv[0], argv[1]); local_exit(-1); } b = clock (); fprintf (stderr, " Time to read the image: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC); /* Make a cbf version of the image */ a = clock (); /* Create the cbf */ cbf_failnez (cbf_make_handle (&cbf)) /* Make a new data block */ cbf_failnez (cbf_new_datablock (cbf, "image_1")) imageno = 0; cbf_failnez (cbf_require_category (cbf, "array_data")) do { char buffer[40]; char * headstring; size_t headsize, nheadsize; unsigned int rows; tstrip_t nstrips, strip; tsize_t stripsize; size_t totread; int elsize, elsign, real, plex, treturn; uint16 sampleformat, samplesperpixel, bitspersample, planarconfig; size_t dimslow, dimmid, dimfast; plex = 1; real = 0; elsign = 0; imageno++; /* bump the image number, starting with 1 versus the tiff directory number that starts with zero */ /* Make or add to the _array_data category */ cbf_failnez (cbf_require_column (cbf, "header_convention")) cbf_failnez (cbf_count_rows (cbf, &rows)) while (imageno >=0 && rows < (unsigned int)imageno) { cbf_failnez (cbf_new_row (cbf)) rows++; } cbf_failnez (cbf_select_row (cbf,imageno-1)) cbf_failnez (cbf_set_value (cbf, "TIFF")) cbf_failnez (cbf_require_column (cbf, "array_id")) sprintf(buffer,"image_%d",imageno); cbf_failnez (cbf_set_value (cbf, buffer)) cbf_failnez (cbf_require_column (cbf, "binary_id")) cbf_failnez (cbf_set_integervalue (cbf, imageno)) cbf_failnez (cbf_require_column (cbf, "header_contents")) headsize = 1+TIFFSNPrintDirectory(tif,buffer,0,TIFFPRINT_COLORMAP|TIFFPRINT_CURVES); headstring = (char *) _TIFFmalloc(headsize); if (!headstring) { cbf_failnez(CBF_ALLOC); } nheadsize = TIFFSNPrintDirectory(tif,headstring,headsize-1,TIFFPRINT_COLORMAP|TIFFPRINT_CURVES); if (nheadsize > headsize-1) { _TIFFfree(headstring); cbf_failnez(CBF_ALLOC); } cbf_onfailnez(cbf_set_value (cbf,headstring),_TIFFfree(headstring)); _TIFFfree(headstring); cbf_failnez (cbf_require_column (cbf, "data")) treturn = TIFFGetField(tif, TIFFTAG_IMAGEWIDTH, &width); if (treturn != 1) cbf_failnez(CBF_ARGUMENT); dimfast = width; treturn = TIFFGetField(tif, TIFFTAG_IMAGELENGTH, &height); if (treturn != 1) cbf_failnez(CBF_ARGUMENT); dimmid = height; dimslow = 1; treturn = TIFFGetField(tif, TIFFTAG_SAMPLEFORMAT, &sampleformat); if (treturn != 1) { sampleformat = SAMPLEFORMAT_UINT; } treturn = TIFFGetField(tif, TIFFTAG_SAMPLESPERPIXEL, &samplesperpixel); if (treturn != 1) samplesperpixel = 1; /* cbf_failnez(CBF_ARGUMENT);*/ treturn = TIFFGetField(tif, TIFFTAG_BITSPERSAMPLE, &bitspersample); if (treturn != 1) cbf_failnez(CBF_ARGUMENT); treturn = TIFFGetField(tif, TIFFTAG_PLANARCONFIG, &planarconfig); if (treturn != 1) planarconfig = PLANARCONFIG_CONTIG; /* cbf_failnez(CBF_ARGUMENT); */ switch ( bitspersample ) { case 8: elsize = 1; break; case 16: elsize = 2; break; case 32: elsize = 4; break; case 64: elsize = 8; break; default: cbf_failnez(CBF_FORMAT); } switch ( sampleformat ) { case SAMPLEFORMAT_UINT: elsign = 0; real = 0; plex = 1; break; /* !unsigned integer data */ case SAMPLEFORMAT_INT: elsign = 1; real = 0; plex = 1; break; /* !signed integer data */ case SAMPLEFORMAT_IEEEFP: elsign = 1; real = 1; plex = 1; break; /* !IEEE floating point data */ case SAMPLEFORMAT_VOID: cbf_failnez(CBF_FORMAT); /* !untyped data */ case SAMPLEFORMAT_COMPLEXINT: elsign = 1; real = 0; plex = 2; elsize /=2; break; /* !complex signed int */ case SAMPLEFORMAT_COMPLEXIEEEFP:elsign = 1; real = 1; plex = 2; elsize /=2; break; /* !complex ieee floating */ default: cbf_failnez(CBF_FORMAT); } switch ( planarconfig ) { case PLANARCONFIG_CONTIG: plex *= samplesperpixel; samplesperpixel = 1; if (plex > 1) { dimslow = dimmid; dimmid = dimfast; dimfast = plex; } break; case PLANARCONFIG_SEPARATE: if (plex > 1 && samplesperpixel > 1) { dimfast = dimfast*plex; dimslow = samplesperpixel; } else if (plex == 1 && samplesperpixel > 1 ) { dimslow = samplesperpixel; } else if (plex > 1 && samplesperpixel == 1) { dimslow = dimmid; dimmid = dimfast; dimfast = plex; } } npixels = dimslow*dimmid*dimfast; nstrips = TIFFNumberOfStrips(tif); stripsize = TIFFStripSize(tif); raster = (unsigned char *) _TIFFmalloc(stripsize*nstrips+stripsize-1); elsize = stripsize*nstrips/npixels; totread = 0; for (strip = 0; strip < nstrips; strip++) { totread +=TIFFReadEncodedStrip(tif, strip, raster+strip*stripsize, stripsize); } if(real){ cbf_failnez (cbf_set_realarray_wdims_fs (cbf, CBF_NONE, imageno, (void *)raster, elsize, npixels, "little_endian",dimfast,dimmid,dimslow,0 )) } else { cbf_failnez (cbf_set_integerarray_wdims_fs (cbf, CBF_NONE, imageno, (void *)raster, elsize, elsign, npixels, "little_endian",dimfast,dimmid,dimslow,0 )) } _TIFFfree(raster); } while (TIFFReadDirectory(tif)); /* Write the new file */ out = fopen (argv [2], "w+b"); if (!out) { fprintf (stderr, " Couldn't open the CBF file %s\n", argv [2]); exit (1); } cbf_failnez (cbf_write_file (cbf, out, 1, CBF, MSG_DIGEST | MIME_HEADERS , 0)) /* Free the cbf */ cbf_failnez (cbf_free_handle (cbf)) b = clock (); fprintf (stderr, " Time to write the CBF image: %.3fs\n", ((b - a) * 1.0) / CLOCKS_PER_SEC); /* Free the tiff images */ TIFFClose(tif); /* Success */ return 0; }