works!

just needs some tests

could be faster too

ChangeLog

@@ -31,6 +31,7 @@
 - add Mitchell kernel
 - pyramid builders have a choice of 2x2 shrinkers [harukizaemon]
 - add `palette` option to pngsave [felixbuenemann]
+- add basic nifti load/save support
 
 12/3/18 started 8.6.4
 - better fitting of fonts with overhanging edges [Adrià]

libvips/foreign/niftiload.c

@@ -103,6 +103,43 @@ vips_foreign_load_nifti_dispose( GObject *gobject )
 		dispose( gobject );
 }
 
+static int
+vips_foreign_load_nifti_is_a( const char *filename )
+{
+	char *hfile;
+	znzFile fp;
+	nifti_1_header nhdr;
+
+	/* Unfortunately is_nifti_file() is very slow and produces lots of
+	 * output. We have to make our own.
+	 */
+
+	if( !(hfile = nifti_findhdrname( filename )) )
+		return( 0 );
+
+	fp = znzopen( hfile, "rb", nifti_is_gzfile( hfile ));
+	if( znz_isnull( fp ) ) { 
+		free( hfile );
+		return( 0 );
+	}
+	free( hfile );
+
+	(void) znzread( &nhdr, 1, sizeof( nhdr ), fp );
+
+	znzclose( fp );
+
+	/* Test for sanity both ways around. There's a thing to test for byte
+	 * order in niftilib, but it's static :(
+	 */
+	if( nifti_hdr_looks_good( &nhdr ) ) 
+		return( 1 );
+	swap_nifti_header( &nhdr, FALSE );
+	if( nifti_hdr_looks_good( &nhdr ) ) 
+		return( 1 );
+
+	return( 0 );
+}
+
 /* Map DT_* datatype values to VipsBandFormat.
  */
 typedef struct _VipsForeignDT2Vips {
@@ -360,7 +397,7 @@ vips_foreign_load_nifti_set_header( VipsForeignLoadNifti *nifti,
 			nim->ndim ); 
 		return( 0 );
 	}
-	for( i = 1; i < 8; i++ ) {
+	for( i = 1; i < 8 && i < nim->ndim + 1; i++ ) {
 		if( nim->dim[i] <= 0 ) {
 			vips_error( class->nickname, 
 				"%s", _( "invalid dimension" ) ); 
@@ -368,7 +405,7 @@ vips_foreign_load_nifti_set_header( VipsForeignLoadNifti *nifti,
 		}
 
 		/* If we have several images in a dimension, the spacing must
-		 * be non-zero, or we'll get a /0 error in resolution
+		 * be non-zero or we'll get a /0 error in resolution
 		 * calculation.
 		 */
 		if( nim->dim[i] > 1 && 
@@ -385,7 +422,7 @@ vips_foreign_load_nifti_set_header( VipsForeignLoadNifti *nifti,
 	bands = 1;
 	width = (guint) nim->nx;
 	height = (guint) nim->ny;
-	for( i = 3; i < 8; i++ )
+	for( i = 3; i < 8 && i < nim->ndim + 1; i++ )
 		if( !g_uint_checked_mul( &height, height, nim->dim[i] ) ) {
 			vips_error( class->nickname, 
 				"%s", _( "dimension overflow" ) ); 
@@ -568,7 +605,7 @@ vips_foreign_load_nifti_class_init( VipsForeignLoadNiftiClass *class )
 
 	foreign_class->suffs = vips__nifti_suffs;
 
-	load_class->is_a = is_nifti_file;
+	load_class->is_a = vips_foreign_load_nifti_is_a;
 	load_class->header = vips_foreign_load_nifti_header;
 	load_class->load = vips_foreign_load_nifti_load;
 

libvips/foreign/niftisave.c

@@ -86,7 +86,73 @@ static int
 vips_foreign_save_nifti_header_vips( VipsForeignSaveNifti *nifti, 
 	VipsImage *image )
 {
-	g_assert( FALSE );
+	VipsObjectClass *class = VIPS_OBJECT_GET_CLASS( nifti );
+
+	int dims[8];
+	int datatype;
+	int i;
+
+	/* Most nifti images have this defaulted as 1.
+	 */
+	for( i = 0; i < VIPS_NUMBER( dims ); i++ )
+		dims[i] = 1;
+
+	dims[0] = 2;
+	dims[1] = image->Xsize;
+	dims[2] = image->Ysize;
+
+	if( vips_image_get_typeof( image, VIPS_META_PAGE_HEIGHT ) ) { 
+		int page_height;
+
+		if( vips_image_get_int( image, 
+			VIPS_META_PAGE_HEIGHT, &page_height ) ) 
+			return( -1 ); 	
+
+		if( image->Ysize % page_height == 0 ) {
+			dims[0] = 3;
+			dims[2] = page_height;
+			dims[3] = image->Ysize / page_height;
+		}
+	}
+
+	datatype = vips__foreign_nifti_BandFmt2datatype( image->BandFmt ); 
+	if( datatype == -1 ) {
+		vips_error( class->nickname, 
+			"%s", _( "unsupported libvips image type" ) );
+		return( -1 );
+	}
+
+	if( image->Bands > 1 ) {
+		if( image->BandFmt != VIPS_FORMAT_UCHAR ) {
+			vips_error( class->nickname, 
+				"%s", _( "8-bit colour images only" ) );
+			return( -1 );
+		}
+
+		if( image->Bands == 3 ) 
+			datatype = DT_RGB;
+		else if( image->Bands == 4 ) 
+			datatype = DT_RGBA32;
+		else {
+			vips_error( class->nickname, 
+				"%s", _( "3 or 4 band colour images only" ) );
+			return( -1 );
+		}
+	}
+
+	if( !(nifti->nim = nifti_make_new_nim( dims, datatype, FALSE )) )
+		return( -1 );
+
+	nifti->nim->dx = 1.0 / image->Xres;
+	nifti->nim->dy = 1.0 / image->Yres;
+	nifti->nim->dz = 1.0 / image->Yres;
+	nifti->nim->xyz_units = NIFTI_UNITS_MM;
+
+	vips_snprintf( nifti->nim->descrip, sizeof( nifti->nim->descrip ),
+		"libvips-%s", VIPS_VERSION ); 
+
+	/* All other fields can stay at their default value.
+	 */
 
 	return( 0 );
 }
@@ -183,6 +249,11 @@ vips_foreign_save_nifti_header_nifti( VipsForeignSaveNifti *nifti,
 	guint height;
 	int i;
 
+	/* Most nifti images have this defaulted as 1.
+	 */
+	for( i = 0; i < VIPS_NUMBER( dims ); i++ )
+		dims[i] = 1;
+
 	info.image = image;
 	info.dims = dims;
 	info.n = 0;
@@ -190,8 +261,22 @@ vips_foreign_save_nifti_header_nifti( VipsForeignSaveNifti *nifti,
 		vips_foreign_save_nifti_set_dims, &info, NULL ) )
 		return( -1 ); 
 
-	/* FIXME what about page-height? should check that too.
+	/* page-height overrides ny if it makes sense. This might not be
+	 * correct :( 
 	 */
+	if( vips_image_get_typeof( image, VIPS_META_PAGE_HEIGHT ) ) { 
+		int page_height;
+
+		if( vips_image_get_int( image, 
+			VIPS_META_PAGE_HEIGHT, &page_height ) ) 
+			return( -1 ); 	
+
+		if( image->Ysize % page_height == 0 ) {
+			dims[0] = 3;
+			dims[2] = page_height;
+			dims[3] = image->Ysize / page_height;
+		}
+	}
 
 	height = 1;
 	for( i = 2; i < VIPS_NUMBER( dims ) && i < dims[0] + 1; i++ )