504 lines
14 KiB
C
504 lines
14 KiB
C
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// Copyright (c) 2005-2008 ASCLEPIOS Project, INRIA Sophia-Antipolis (France)
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// All rights reserved.
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//
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// This file is part of the ImageIO Library, and as been adapted for
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// CGAL (www.cgal.org).
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// You can redistribute it and/or modify it under the terms of the
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// GNU Lesser General Public License as published by the Free Software Foundation;
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// either version 3 of the License, or (at your option) any later version.
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//
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// Licensees holding a valid commercial license may use this file in
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// accordance with the commercial license agreement provided with the software.
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//
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// These files are provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
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// WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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//
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// $URL$
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// $Id$
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// SPDX-License-Identifier: LGPL-3.0+
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//
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//
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// Author(s) : ASCLEPIOS Project (INRIA Sophia-Antipolis), Laurent Rineau
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#ifdef CGAL_HEADER_ONLY
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#define CGAL_INLINE_FUNCTION inline
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#else
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#define CGAL_INLINE_FUNCTION
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#endif
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#ifdef _MSC_VER
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#pragma warning ( disable : 4068 4786 4081 )
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#endif
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#ifdef MINC_FILES
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#include <math.h>
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#include <sys/types.h>
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#include <sys/stat.h>
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#include <unistd.h>
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/** Magic header for MINC (MNI NetCDF) file format */
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#ifdef MINC_FILES
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# define MINC_MAGIC "CDF"
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#endif
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CGAL_INLINE_FUNCTION
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int readMincHeader(_image *im, const char* filename,
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double *startx, double *starty, double *startz,
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double *stepx, double *stepy, double *stepz,
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double *Xcosines, double *Ycosines, double *Zcosines) {
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int fin, varid, minc_icv, id, ndims, i, dim[256], length,
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minfound = 0, maxfound = 0;
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long start[3] = {0, 0, 0}, count[3];
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unsigned int plane1, plane2, line, shift[3], ct[3];
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nc_type type;
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char sign_type[MI_MAX_ATTSTR_LEN], name[MAX_NC_NAME];
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void *data;
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double range[2], swap;
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/* open minc file */
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fin = miopen((char *) filename, NC_NOWRITE);
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if(fin == MI_ERROR) return 0;
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/* get number of dimensions and type */
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id = ncvarid(fin, MIimage);
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(void) ncvarinq(fin, id, NULL, &type, &ndims, dim, NULL);
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if(ndims != 3) {
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fprintf(stderr, "unsupported %i dimensional minc file\n", ndims);
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return 0;
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}
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/* get sign */
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if ((miattgetstr(fin, id, MIsigntype, MI_MAX_ATTSTR_LEN, sign_type)
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== NULL) || ((strcmp(sign_type, MI_UNSIGNED)!=0) &&
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(strcmp(sign_type, MI_SIGNED)!=0))) {
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if (type == NC_BYTE)
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(void) strcpy(sign_type, MI_UNSIGNED);
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else
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(void) strcpy(sign_type, MI_SIGNED);
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}
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im->sign = (!strcmp(sign_type, MI_UNSIGNED)) ? SGN_UNSIGNED : SGN_SIGNED;
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switch(type) {
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case NC_CHAR:
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case NC_BYTE:
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im->wdim = 1;
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im->wordKind = WK_FIXED;
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im->sign = SGN_UNSIGNED;
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break;
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case NC_SHORT:
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im->wdim = 2;
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im->wordKind = WK_FIXED;
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break;
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case NC_LONG:
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im->wdim = 4;
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im->wordKind = WK_FIXED;
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break;
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case NC_FLOAT:
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im->wdim = 4;
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im->wordKind = WK_FLOAT;
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im->sign = SGN_UNKNOWN;
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break;
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case NC_DOUBLE:
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im->wdim = 8;
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im->wordKind = WK_FLOAT;
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im->sign = SGN_UNKNOWN;
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break;
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default:
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fprintf(stderr, "unsupported minc type\n");
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return 0;
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break;
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}
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/* get dimensions length and voxel size */
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ncopts = 0;
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for(i = 0; i < ndims; i++) {
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(void) ncdiminq(fin, dim[i], name, &count[i]);
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varid = ncvarid(fin, name);
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if(!strcmp(name, MIxspace)) {
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im->xdim = count[i];
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if(miattget1(fin, varid, MIstep, NC_DOUBLE, stepx) == MI_ERROR)
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*stepx = 1.0;
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im->vx = fabs(*stepx);
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if(miattget1(fin, varid, MIstart, NC_DOUBLE, startx) == MI_ERROR)
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*startx = 0.0;
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if(miattget(fin, varid, MIdirection_cosines, NC_DOUBLE, 3,
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(void *) Xcosines, (int *) 0) == MI_ERROR ) {
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Xcosines[0] = 0.0;
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Xcosines[1] = 0.0;
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Xcosines[2] = 0.0;
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}
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}
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else if(!strcmp(name, MIyspace)) {
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im->ydim = count[i];
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if(miattget1(fin, varid, MIstep, NC_DOUBLE, stepy) == MI_ERROR)
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*stepy = 1.0;
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im->vy = fabs(*stepy);
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if(miattget1(fin, varid, MIstart, NC_DOUBLE, starty) == MI_ERROR)
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*starty = 0.0;
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if(miattget(fin, varid, MIdirection_cosines, NC_DOUBLE, 3,
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(void *) Ycosines, (int *) 0) == MI_ERROR ) {
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Ycosines[0] = 0.0;
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Ycosines[1] = 0.0;
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Ycosines[2] = 0.0;
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}
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}
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else if(!strcmp(name, MIzspace)) {
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im->zdim = count[i];
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if(miattget1(fin, varid, MIstep, NC_DOUBLE, stepz) == MI_ERROR)
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*stepz = 1.0;
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im->vz = fabs(*stepz);
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if(miattget1(fin, varid, MIstart, NC_DOUBLE, startz) == MI_ERROR)
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*startz = 0.0;
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if(miattget(fin, varid, MIdirection_cosines, NC_DOUBLE, 3,
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(void *) Zcosines, (int *) 0) == MI_ERROR ) {
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Zcosines[0] = 0.0;
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Zcosines[1] = 0.0;
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Zcosines[2] = 0.0;
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}
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} else {
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fprintf(stderr, "unsupported dimension %s\n", name);
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return 0;
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}
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}
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if( miattget( fin, id, MIvalid_range, NC_DOUBLE, 2,
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(void *) range, &length) == MI_ERROR || length != 2 ) {
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if( miattget1( fin, id, MIvalid_min, NC_DOUBLE,
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(void *) &range[0] ) != MI_ERROR )
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minfound = 1;
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if( miattget1( fin, id, MIvalid_max, NC_DOUBLE,
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(void *) &range[1] ) != MI_ERROR )
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maxfound = 1;
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}
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else {
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if( range[0] > range[1] ) {
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swap = range[0];
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range[0] = range[1];
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range[1] = swap;
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}
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minfound = 1;
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maxfound = 1;
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}
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if(!minfound) {
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switch(type) {
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case NC_CHAR:
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case NC_BYTE:
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range[0] = 0;
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break;
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case NC_SHORT:
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if(im->sign == SGN_SIGNED) range[0] = -32768.0;
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else range[0] = 0;
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break;
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case NC_LONG:
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if(im->sign == SGN_SIGNED) range[0] = -2147483648.0;
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else range[0] = 0;
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break;
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default:
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range[0] = 0.0;
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break;
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}
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}
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if(!maxfound) {
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switch(type) {
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case NC_CHAR:
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case NC_BYTE:
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range[1] = 255.0;
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break;
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case NC_SHORT:
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if(im->sign == SGN_SIGNED) range[1] = 32767.0;
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else range[1] = 65535.0;
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break;
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case NC_LONG:
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if(im->sign == SGN_SIGNED) range[1] = 2147483647.0;
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else range[1] = 4294967295.0;
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break;
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default:
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range[1] = 1.0;
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break;
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}
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}
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ncopts = NC_VERBOSE | NC_FATAL;
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im->vdim = 1;
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/* read data bytes */
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im->data = ImageIO_alloc(im->xdim * im->ydim * im->zdim * im->vdim *
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im->wdim);
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minc_icv = miicv_create();
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(void) miicv_setint( minc_icv, MI_ICV_TYPE, type );
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(void) miicv_setstr( minc_icv, MI_ICV_SIGN, sign_type );
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(void) miicv_setint( minc_icv, MI_ICV_DO_NORM, 1 );
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(void) miicv_setint( minc_icv, MI_ICV_DO_FILLVALUE, 1 );
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(void) miicv_setdbl( minc_icv, MI_ICV_VALID_MIN, range[0] );
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(void) miicv_setdbl( minc_icv, MI_ICV_VALID_MAX, range[1] );
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(void) miicv_attach( minc_icv, fin, id );
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if(miicv_get(minc_icv, start, count, im->data) == MI_ERROR) {
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fprintf(stderr, "error while reading file\n");
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return 0;
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}
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(void) miicv_detach( minc_icv );
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(void) miicv_free( minc_icv );
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ImageIO_closeImage(im);
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/* order data in ZYX */
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(void) ncdiminq(fin, dim[0], name, NULL);
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if(!strcmp(name, MIzspace)) {
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(void) ncdiminq(fin, dim[1], name, NULL);
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/* file is ZYX */
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if(!strcmp(name, MIyspace)) {
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miclose(fin);
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return 1;
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}
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}
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(void) ncdiminq(fin, dim[0], name, NULL);
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/* file is ZXY */
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if(!strcmp(name, MIzspace)) {
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shift[0] = 0;
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shift[1] = 2;
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shift[2] = 1;
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plane2 = im->xdim * im->ydim;
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line = im->ydim;
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}
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/* file is Y first */
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else if(!strcmp(name, MIyspace)) {
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shift[0] = 1;
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plane2 = im->xdim * im->zdim;
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(void) ncdiminq(fin, dim[1], name, NULL);
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/* file is YXZ */
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if(!strcmp(name, MIxspace)) {
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shift[1] = 2;
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shift[2] = 0;
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line = im->zdim;
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}
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/* file is YZX */
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else {
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shift[1] = 0;
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shift[2] = 2;
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line = im->xdim;
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}
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}
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/* file is X first */
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else {
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shift[0] = 2;
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plane2 = im->ydim * im->zdim;
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(void) ncdiminq(fin, dim[1], name, NULL);
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/* file is XYZ */
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if(!strcmp(name, MIyspace)) {
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shift[1] = 1;
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shift[2] = 0;
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line = im->zdim;
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}
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/* file is XZY */
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else {
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shift[1] = 0;
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shift[2] = 1;
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line = im->ydim;
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}
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}
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data = ImageIO_alloc(im->xdim * im->ydim * im->zdim * im->vdim * im->wdim);
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plane1 = im->xdim * im->ydim;
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for(ct[0] = 0; ct[0] < im->zdim; ct[0]++) {
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for(ct[1] = 0; ct[1] < im->ydim; ct[1]++) {
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for(ct[2] = 0; ct[2] < im->xdim; ct[2]++) {
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memcpy((unsigned char *) data +
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(ct[0] * plane1 + ct[1] * im->xdim + ct[2]) * im->wdim,
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(unsigned char *) im->data +
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(ct[shift[0]] * plane2 + ct[shift[1]] * line + ct[shift[2]])
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* im->wdim, im->wdim);
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}
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}
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}
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ImageIO_free(im->data);
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im->data = data;
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/* close file */
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miclose(fin);
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return 1;
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}
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CGAL_INLINE_FUNCTION
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int writeMincFile( const _image* im, const char *filename,
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const char *sourcename,
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double startx, double starty, double startz,
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double stepx, double stepy, double stepz,
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const double *Xcosine, const double *Ycosine,
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const double *Zcosine, const double *range ) {
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int i, cdfid, minc_icv, dim_vars[3], dim_ids[3], img_var_id, min_id, max_id,
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src_cdfid, src_img_var, varid, n_excluded, excluded_vars[10],
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src_min_id, src_max_id, src_root_id, old_att_length, same_file = 0;
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long org[3] = {0, 0, 0}, count[3] = { im->zdim, im->ydim, im->xdim };
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char *dim_names[3] = { MIzspace, MIyspace, MIxspace }, *history,
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*excluded_list[3] = { MIxspace, MIyspace, MIzspace }, *newname;
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nc_type type, datatype;
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double start[3] = { startz, starty, startx },
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vx[3] = { stepz, stepy, stepx };
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|
||
|
|
/* if filename is the same file that sourcename, it is needed to create
|
||
|
|
a temporary file for output */
|
||
|
|
newname = (char *) filename;
|
||
|
|
if(sourcename) {
|
||
|
|
struct stat out, org;
|
||
|
|
same_file = (stat(sourcename, &org) == 0) && (stat(filename, &out) == 0)
|
||
|
|
&& (org.st_ino == out.st_ino);
|
||
|
|
if(same_file) {
|
||
|
|
newname = (char *) malloc((strlen(filename) + 10) * sizeof(char));
|
||
|
|
for(i = strlen(filename) - 1; i > 0 && filename[i] != '/'; i--) ;
|
||
|
|
if(filename[i] == '/') {
|
||
|
|
strncpy(newname, filename, i + 1);
|
||
|
|
newname[i+1] = '\0';
|
||
|
|
strcat(newname, "#TMP#");
|
||
|
|
strcat(newname, filename + i + 1);
|
||
|
|
}
|
||
|
|
else
|
||
|
|
sprintf(newname, "#TMP#%s", filename);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
/* open file */
|
||
|
|
cdfid = micreate( (char *) newname, NC_CLOBBER );
|
||
|
|
if( cdfid == MI_ERROR ) {
|
||
|
|
fprintf(stderr, "Error: opening MINC file \"%s\".\n", filename );
|
||
|
|
return -1;
|
||
|
|
}
|
||
|
|
|
||
|
|
/* set word type */
|
||
|
|
switch(im->wordKind) {
|
||
|
|
case WK_FIXED:
|
||
|
|
if(im->wdim == 1) type = NC_BYTE;
|
||
|
|
else if(im->wdim == 2) type = NC_SHORT;
|
||
|
|
else type = NC_LONG;
|
||
|
|
break;
|
||
|
|
case WK_FLOAT:
|
||
|
|
default:
|
||
|
|
if(im->wdim == 4) type = NC_FLOAT;
|
||
|
|
else type = NC_DOUBLE;
|
||
|
|
break;
|
||
|
|
}
|
||
|
|
|
||
|
|
/* create dimensions variables */
|
||
|
|
for(i = 0; i < 3; i++)
|
||
|
|
dim_vars[i] = ncdimdef( cdfid, dim_names[i], count[i] );
|
||
|
|
|
||
|
|
for(i = 0; i < 3; i++ ) {
|
||
|
|
dim_ids[i] = micreate_std_variable( cdfid, dim_names[i], NC_DOUBLE,
|
||
|
|
0, NULL);
|
||
|
|
if( dim_ids[i] < 0 ) return -1;
|
||
|
|
(void) miattputdbl( cdfid, dim_ids[i], MIstep, vx[i]);
|
||
|
|
(void) miattputdbl( cdfid, dim_ids[i], MIstart, start[i]);
|
||
|
|
}
|
||
|
|
if(Zcosine[0] != 0.0 || Zcosine[1] != 0.0 || Zcosine[2] != 0.0)
|
||
|
|
(void) ncattput(cdfid, dim_ids[0], MIdirection_cosines, NC_DOUBLE, 3,
|
||
|
|
Zcosine);
|
||
|
|
if(Ycosine[0] != 0.0 || Ycosine[1] != 0.0 || Ycosine[2] != 0.0)
|
||
|
|
(void) ncattput(cdfid, dim_ids[1], MIdirection_cosines, NC_DOUBLE, 3,
|
||
|
|
Ycosine);
|
||
|
|
if(Xcosine[0] != 0.0 || Xcosine[1] != 0.0 || Xcosine[2] != 0.0)
|
||
|
|
(void) ncattput(cdfid, dim_ids[2], MIdirection_cosines, NC_DOUBLE, 3,
|
||
|
|
Xcosine);
|
||
|
|
|
||
|
|
/* create image variable */
|
||
|
|
img_var_id = micreate_std_variable( cdfid, MIimage, type, 3, dim_vars );
|
||
|
|
(void) miattputstr( cdfid, img_var_id, MIcomplete, MI_FALSE );
|
||
|
|
if(im->sign == SGN_SIGNED)
|
||
|
|
(void) miattputstr( cdfid, img_var_id, MIsigntype, MI_SIGNED );
|
||
|
|
else
|
||
|
|
(void) miattputstr( cdfid, img_var_id, MIsigntype, MI_UNSIGNED );
|
||
|
|
(void) ncattput(cdfid, img_var_id, MIvalid_range ,NC_DOUBLE, 2, range);
|
||
|
|
|
||
|
|
min_id = micreate_std_variable(cdfid, MIimagemin, NC_DOUBLE, 0, 0 );
|
||
|
|
max_id = micreate_std_variable(cdfid, MIimagemax, NC_DOUBLE, 0, 0 );
|
||
|
|
|
||
|
|
/* if the image comes from a minc file, duplicate all minc attributes */
|
||
|
|
if(sourcename) {
|
||
|
|
if( (src_cdfid = miopen((char *) sourcename, NC_NOWRITE)) == MI_ERROR ) {
|
||
|
|
fprintf(stderr, "Error opening %s\n", sourcename );
|
||
|
|
return -1;
|
||
|
|
}
|
||
|
|
|
||
|
|
n_excluded = 0;
|
||
|
|
for( i = 0; i < 3; i++ ) {
|
||
|
|
if( (varid = ncvarid(src_cdfid, excluded_list[i] )) != MI_ERROR )
|
||
|
|
excluded_vars[n_excluded++] = varid;
|
||
|
|
}
|
||
|
|
|
||
|
|
if( (src_img_var = ncvarid(src_cdfid, MIimage )) != MI_ERROR )
|
||
|
|
excluded_vars[n_excluded++] = src_img_var;
|
||
|
|
if( (src_max_id = ncvarid(src_cdfid, MIimagemax )) != MI_ERROR )
|
||
|
|
excluded_vars[n_excluded++] = src_max_id;
|
||
|
|
if( (src_min_id = ncvarid(src_cdfid, MIimagemin )) != MI_ERROR )
|
||
|
|
excluded_vars[n_excluded++] = src_min_id;
|
||
|
|
if( (src_root_id = ncvarid(src_cdfid, MIrootvariable )) != MI_ERROR )
|
||
|
|
excluded_vars[n_excluded++] = src_root_id;
|
||
|
|
|
||
|
|
(void) micopy_all_var_defs( src_cdfid, cdfid, n_excluded, excluded_vars );
|
||
|
|
|
||
|
|
if( src_img_var != MI_ERROR )
|
||
|
|
(void) micopy_all_atts( src_cdfid, src_img_var, cdfid, img_var_id );
|
||
|
|
if( src_root_id != MI_ERROR )
|
||
|
|
(void) micopy_all_atts( src_cdfid, src_root_id, cdfid,
|
||
|
|
ncvarid( cdfid, MIrootvariable) );
|
||
|
|
|
||
|
|
ncopts = 0;
|
||
|
|
if(ncattinq(cdfid, NC_GLOBAL, MIhistory, &datatype, &old_att_length)
|
||
|
|
== MI_ERROR || datatype != NC_CHAR )
|
||
|
|
old_att_length = 0;
|
||
|
|
|
||
|
|
history = (char *) malloc(sizeof(char) * old_att_length);
|
||
|
|
history[0] = (char) 0;
|
||
|
|
(void) miattgetstr( cdfid, NC_GLOBAL, MIhistory, old_att_length+1,
|
||
|
|
history );
|
||
|
|
ncopts = NC_VERBOSE | NC_FATAL;
|
||
|
|
(void) miattputstr( cdfid, NC_GLOBAL, MIhistory, history );
|
||
|
|
free(history);
|
||
|
|
|
||
|
|
(void) miclose( src_cdfid );
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
/* write data */
|
||
|
|
if(ncendef(cdfid) == MI_ERROR) return -1;
|
||
|
|
minc_icv = miicv_create();
|
||
|
|
(void) miicv_setint( minc_icv, MI_ICV_TYPE, type);
|
||
|
|
(void) miicv_setstr( minc_icv, MI_ICV_SIGN,
|
||
|
|
(im->sign == SGN_SIGNED) ? MI_SIGNED : MI_UNSIGNED );
|
||
|
|
(void) miicv_setint( minc_icv, MI_ICV_DO_NORM, 1 );
|
||
|
|
(void) miicv_setint( minc_icv, MI_ICV_USER_NORM, 1 );
|
||
|
|
(void) miicv_attach( minc_icv, cdfid, img_var_id );
|
||
|
|
|
||
|
|
if( miicv_put(minc_icv, org, count, im->data) == MI_ERROR )
|
||
|
|
return -1;
|
||
|
|
|
||
|
|
(void) miattputstr( cdfid, img_var_id, MIcomplete, MI_TRUE);
|
||
|
|
(void) miclose( cdfid );
|
||
|
|
(void) miicv_free( minc_icv );
|
||
|
|
|
||
|
|
if(same_file) {
|
||
|
|
unlink(filename);
|
||
|
|
link(newname, filename);
|
||
|
|
unlink(newname);
|
||
|
|
free(newname);
|
||
|
|
}
|
||
|
|
|
||
|
|
return 0;
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
#endif
|