483 lines
11 KiB
C
483 lines
11 KiB
C
/* save to nifti
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*
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* 5/7/18
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* - from fitssave.c
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* 9/9/19
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* - use double for all floating point scalar metadata, like other loaders
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*/
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/*
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This file is part of VIPS.
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VIPS is free software; you can redistribute it and/or modify
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it under the terms of the GNU Lesser General Public License as published by
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the Free Software Foundation; either version 2 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public License
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along with this program; if not, write to the Free Software
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Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
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02110-1301 USA
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*/
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/*
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These files are distributed with VIPS - http://www.vips.ecs.soton.ac.uk
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*/
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/*
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#define DEBUG_VERBOSE
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#define DEBUG
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*/
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#ifdef HAVE_CONFIG_H
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#include <config.h>
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#endif /*HAVE_CONFIG_H*/
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#include <glib/gi18n-lib.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <vips/vips.h>
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#ifdef HAVE_NIFTI
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#include <nifti1_io.h>
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#include "pforeign.h"
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typedef struct _VipsForeignSaveNifti {
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VipsForeignSave parent_object;
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/* Filename for save.
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*/
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char *filename;
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nifti_image *nim;
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} VipsForeignSaveNifti;
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typedef VipsForeignSaveClass VipsForeignSaveNiftiClass;
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G_DEFINE_TYPE( VipsForeignSaveNifti, vips_foreign_save_nifti,
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VIPS_TYPE_FOREIGN_SAVE );
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static void
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vips_foreign_save_nifti_dispose( GObject *gobject )
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{
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VipsForeignSaveNifti *nifti = (VipsForeignSaveNifti *) gobject;
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VIPS_FREEF( nifti_image_free, nifti->nim );
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G_OBJECT_CLASS( vips_foreign_save_nifti_parent_class )->
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dispose( gobject );
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}
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/* Make ->nim from the vips header fields.
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*/
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static int
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vips_foreign_save_nifti_header_vips( VipsForeignSaveNifti *nifti,
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VipsImage *image )
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{
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VipsObjectClass *class = VIPS_OBJECT_GET_CLASS( nifti );
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int dims[8];
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int datatype;
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int i;
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/* Most nifti images have this defaulted as 1.
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*/
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for( i = 0; i < VIPS_NUMBER( dims ); i++ )
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dims[i] = 1;
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dims[0] = 2;
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dims[1] = image->Xsize;
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dims[2] = vips_image_get_page_height( image );
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/* Multipage image?
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*/
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if( dims[2] < image->Ysize ) {
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dims[0] = 3;
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dims[3] = image->Ysize / dims[2];
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}
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datatype = vips__foreign_nifti_BandFmt2datatype( image->BandFmt );
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if( datatype == -1 ) {
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vips_error( class->nickname,
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"%s", _( "unsupported libvips image type" ) );
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return( -1 );
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}
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if( image->Bands > 1 ) {
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if( image->BandFmt != VIPS_FORMAT_UCHAR ) {
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vips_error( class->nickname,
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"%s", _( "8-bit colour images only" ) );
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return( -1 );
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}
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if( image->Bands == 3 )
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datatype = DT_RGB;
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else if( image->Bands == 4 )
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datatype = DT_RGBA32;
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else {
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vips_error( class->nickname,
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"%s", _( "3 or 4 band colour images only" ) );
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return( -1 );
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}
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}
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if( !(nifti->nim = nifti_make_new_nim( dims, datatype, FALSE )) )
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return( -1 );
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nifti->nim->dx = 1.0 / image->Xres;
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nifti->nim->dy = 1.0 / image->Yres;
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nifti->nim->dz = 1.0 / image->Yres;
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nifti->nim->xyz_units = NIFTI_UNITS_MM;
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vips_snprintf( nifti->nim->descrip, sizeof( nifti->nim->descrip ),
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"libvips-%s", VIPS_VERSION );
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/* All other fields can stay at their default value.
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*/
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return( 0 );
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}
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typedef struct _VipsNdimInfo {
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VipsImage *image;
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nifti_image *nim;
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int *dims;
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int n;
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} VipsNdimInfo;
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static void *
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vips_foreign_save_nifti_set_dims( const char *name,
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GValue *value, glong offset, void *a, void *b )
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{
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VipsNdimInfo *info = (VipsNdimInfo *) a;
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/* The first 8 members are the dims fields.
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*/
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if( info->n < 8 ) {
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char vips_name[256];
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int i;
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vips_snprintf( vips_name, 256, "nifti-%s", name );
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if( vips_image_get_int( info->image, vips_name, &i ) ||
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i <= 0 ||
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i >= VIPS_MAX_COORD )
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return( info );
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info->dims[info->n] = i;
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}
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info->n += 1;
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return( NULL );
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}
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/* How I wish glib had something like this :( Just implement the ones we need
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* for vips_foreign_nifti_fields above.
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*/
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static void
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vips_gvalue_write( GValue *value, void *p )
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{
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switch( G_VALUE_TYPE( value ) ) {
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case G_TYPE_INT:
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*((int *) p) = g_value_get_int( value );
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break;
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case G_TYPE_DOUBLE:
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*((float *) p) = g_value_get_double( value );
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break;
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default:
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g_warning( "vips_gvalue_write: unsupported GType %s",
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g_type_name( G_VALUE_TYPE( value ) ) );
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}
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}
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static void *
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vips_foreign_save_nifti_set_fields( const char *name,
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GValue *value, glong offset, void *a, void *b )
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{
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VipsNdimInfo *info = (VipsNdimInfo *) a;
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/* The first 8 members are the dims fields. We set them above ^^^ --
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* do the others in this pass.
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*/
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if( info->n >= 8 ) {
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char vips_name[256];
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GValue value_copy = { 0 };
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vips_snprintf( vips_name, 256, "nifti-%s", name );
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if( vips_image_get( info->image, vips_name, &value_copy ) )
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return( info );
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vips_gvalue_write( &value_copy, (gpointer) info->nim + offset );
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g_value_unset( &value_copy );
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}
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info->n += 1;
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return( NULL );
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}
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static void *
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vips_foreign_save_nifti_ext( VipsImage *image,
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const char *field, GValue *value, void *a )
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{
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nifti_image *nim = (nifti_image *) a;
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int i;
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int ecode;
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char *data;
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size_t length;
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if( !vips_isprefix( "nifti-ext-", field ) )
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return( NULL );
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/* The name is "nifti-ext-N-XX" where N is the index (discard this)
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* and XX is the nifti ext ecode.
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*/
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if( sscanf( field, "nifti-ext-%d-%d", &i, &ecode ) != 2 ) {
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vips_error( "niftisave",
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"%s", _( "bad nifti-ext- field name" ) );
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return( image );
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}
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if( vips_image_get_blob( image, field, (void *) &data, &length ) )
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return( image );
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if( nifti_add_extension( nim, data, length, ecode ) ) {
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vips_error( "niftisave",
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"%s", _( "unable to attach nifti ext" ) );
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return( image );
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}
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return( NULL );
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}
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/* Make ->nim from the nifti- fields.
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*/
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static int
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vips_foreign_save_nifti_header_nifti( VipsForeignSaveNifti *nifti,
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VipsImage *image )
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{
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VipsObjectClass *class = VIPS_OBJECT_GET_CLASS( nifti );
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VipsNdimInfo info;
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int dims[8];
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int datatype;
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guint height;
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int i;
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/* Most nifti images have this defaulted as 1.
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*/
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for( i = 0; i < VIPS_NUMBER( dims ); i++ )
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dims[i] = 1;
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info.image = image;
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info.dims = dims;
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info.n = 0;
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if( vips__foreign_nifti_map(
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vips_foreign_save_nifti_set_dims, &info, NULL ) )
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return( -1 );
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/* page-height overrides ny if it makes sense. This might not be
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* correct :(
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*/
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dims[2] = vips_image_get_page_height( image );
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/* Multipage image?
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*/
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if( dims[2] < image->Ysize ) {
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dims[0] = 3;
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dims[3] = image->Ysize / dims[2];
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}
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height = 1;
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for( i = 2; i < VIPS_NUMBER( dims ) && i < dims[0] + 1; i++ )
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if( !g_uint_checked_mul( &height, height, dims[i] ) ) {
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vips_error( class->nickname,
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"%s", _( "dimension overflow" ) );
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return( 0 );
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}
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if( image->Xsize != dims[1] ||
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image->Ysize != height ) {
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vips_error( class->nickname,
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"%s", _( "bad image dimensions" ) );
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return( -1 );
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}
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datatype = vips__foreign_nifti_BandFmt2datatype( image->BandFmt );
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if( datatype == -1 ) {
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vips_error( class->nickname,
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"%s", _( "unsupported libvips image type" ) );
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return( -1 );
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}
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if( !(nifti->nim = nifti_make_new_nim( dims, datatype, FALSE )) )
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return( -1 );
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info.image = image;
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info.nim = nifti->nim;
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info.n = 0;
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if( vips__foreign_nifti_map(
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vips_foreign_save_nifti_set_fields, &info, NULL ) )
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return( -1 );
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/* Attach any ext blocks.
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*/
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if( vips_image_map( image,
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(VipsImageMapFn) vips_foreign_save_nifti_ext, nifti->nim ) )
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return( -1 );
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return( 0 );
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}
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static int
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vips_foreign_save_nifti_build( VipsObject *object )
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{
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VipsObjectClass *class = VIPS_OBJECT_GET_CLASS( object );
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VipsForeignSave *save = (VipsForeignSave *) object;
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VipsForeignSaveNifti *nifti = (VipsForeignSaveNifti *) object;
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if( VIPS_OBJECT_CLASS( vips_foreign_save_nifti_parent_class )->
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build( object ) )
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return( -1 );
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/* This could be an image (indirectly) from niftiload, or something
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* like OME_TIFF, which does not have all the "nifti-ndim" fields.
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*
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* If it doesn't look like a nifti, try to make a nifti header from
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* what we have.
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*/
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if( vips_image_get_typeof( save->ready, "nifti-ndim" ) ) {
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if( vips_foreign_save_nifti_header_nifti( nifti, save->ready ) )
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return( -1 );
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}
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else {
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if( vips_foreign_save_nifti_header_vips( nifti, save->ready ) )
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return( -1 );
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}
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/* set ext, plus other stuff
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*/
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if( nifti_set_filenames( nifti->nim, nifti->filename, FALSE, TRUE ) ) {
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vips_error( class->nickname,
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"%s", _( "unable to set nifti filename" ) );
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return( -1 );
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}
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if( !(nifti->nim->data =
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vips_image_write_to_memory( save->ready, NULL )) )
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return( -1 );
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/* No return code!??!?!!
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*/
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nifti_image_write( nifti->nim );
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/* We must free and NULL the pointer or nifti will try to free it for
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* us.
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*/
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VIPS_FREE( nifti->nim->data );
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return( 0 );
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}
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/* Save a bit of typing.
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*/
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#define UC VIPS_FORMAT_UCHAR
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#define C VIPS_FORMAT_CHAR
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#define US VIPS_FORMAT_USHORT
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#define S VIPS_FORMAT_SHORT
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#define UI VIPS_FORMAT_UINT
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#define I VIPS_FORMAT_INT
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#define F VIPS_FORMAT_FLOAT
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#define X VIPS_FORMAT_COMPLEX
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#define D VIPS_FORMAT_DOUBLE
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#define DX VIPS_FORMAT_DPCOMPLEX
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static int vips_nifti_bandfmt[10] = {
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/* UC C US S UI I F X D DX */
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UC, C, US, S, UI, I, F, X, D, DX
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};
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static void
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vips_foreign_save_nifti_class_init( VipsForeignSaveNiftiClass *class )
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{
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GObjectClass *gobject_class = G_OBJECT_CLASS( class );
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VipsObjectClass *object_class = (VipsObjectClass *) class;
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VipsOperationClass *operation_class = VIPS_OPERATION_CLASS( class );
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VipsForeignClass *foreign_class = (VipsForeignClass *) class;
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VipsForeignSaveClass *save_class = (VipsForeignSaveClass *) class;
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gobject_class->dispose = vips_foreign_save_nifti_dispose;
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gobject_class->set_property = vips_object_set_property;
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gobject_class->get_property = vips_object_get_property;
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object_class->nickname = "niftisave";
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object_class->description = _( "save image to nifti file" );
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object_class->build = vips_foreign_save_nifti_build;
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/* nificlib has not been fuzzed, so should not be used with
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* untrusted input unless you are very careful.
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*/
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operation_class->flags |= VIPS_OPERATION_UNTRUSTED;
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foreign_class->suffs = vips_foreign_nifti_suffs;
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save_class->saveable = VIPS_SAVEABLE_ANY;
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save_class->format_table = vips_nifti_bandfmt;
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VIPS_ARG_STRING( class, "filename", 1,
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_( "Filename" ),
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_( "Filename to save to" ),
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VIPS_ARGUMENT_REQUIRED_INPUT,
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G_STRUCT_OFFSET( VipsForeignSaveNifti, filename ),
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NULL );
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}
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static void
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vips_foreign_save_nifti_init( VipsForeignSaveNifti *nifti )
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{
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}
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#endif /*HAVE_NIFTI*/
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/**
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* vips_niftisave: (method)
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* @in: image to save
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* @filename: file to write to
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* @...: %NULL-terminated list of optional named arguments
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*
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* Write a VIPS image to a file in NIFTI format.
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*
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* Use the various NIFTI suffixes to pick the nifti save format.
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*
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* See also: vips_image_write_to_file(), vips_niftiload().
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*
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* Returns: 0 on success, -1 on error.
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*/
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int
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vips_niftisave( VipsImage *in, const char *filename, ... )
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{
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va_list ap;
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int result;
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va_start( ap, filename );
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result = vips_call_split( "niftisave", ap, in, filename );
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va_end( ap );
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return( result );
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}
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