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/**********************************************************************
* 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 <tiffio.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <time.h>
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;
}
|
