add OpenSlide VipsFormat

Don't export im_openslide2vips, since there's no point in creating new
deprecated API.

libvips/format/Makefile.am

@@ -22,6 +22,7 @@ libformat_la_SOURCES = \
 	im_vips2raw.c \
 	matlab.c \
 	fits.c \
-	radiance.c 
+	radiance.c \
+	openslide.c
 
 INCLUDES = -I${top_srcdir}/libvips/include @VIPS_CFLAGS@ @VIPS_INCLUDES@

libvips/format/format.c

@@ -464,6 +464,10 @@ im__format_init( void )
 	extern GType vips_format_exr_get_type();
 	vips_format_exr_get_type();
 #endif /*HAVE_OPENEXR*/
+#ifdef HAVE_OPENSLIDE
+	extern GType vips_format_openslide_get_type();
+	vips_format_openslide_get_type();
+#endif /*HAVE_OPENSLIDE*/
 #ifdef HAVE_MATIO
 	extern GType vips_format_mat_get_type();
 	vips_format_mat_get_type();

libvips/format/openslide.c

@@ -0,0 +1,247 @@
+/* Read a virtual microscope slide using OpenSlide.
+ *
+ * Benjamin Gilbert
+ *
+ * Copyright (c) 2011 Carnegie Mellon University
+ *
+ * 26/11/11
+ *	- initial version
+ */
+
+/*
+
+    This file is part of VIPS.
+
+    VIPS is free software; you can redistribute it and/or modify
+    it under the terms of the GNU Lesser 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 Lesser General Public License for more details.
+
+    You should have received a copy of the GNU Lesser 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
+
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif /*HAVE_CONFIG_H*/
+
+#ifdef HAVE_OPENSLIDE
+
+#include <string.h>
+#include <stdint.h>
+#include <limits.h>
+#include <openslide.h>
+
+#include <vips/vips.h>
+#include <vips/intl.h>
+
+static void
+close_slide( VipsImage *image, openslide_t *osr )
+{
+	openslide_close( osr );
+}
+
+static int
+load_header( openslide_t *osr, VipsImage *out )
+{
+	int64_t w, h;
+
+	openslide_get_layer0_dimensions( osr, &w, &h );
+	if( w < 0 || h < 0 ) {
+		vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
+			openslide_get_error( osr ));
+		return( -1 );
+	}
+	if( w > INT_MAX || h > INT_MAX ) {
+		vips_error( "im_openslide2vips",
+			_( "image dimensions overflow int" ));
+		return( -1 );
+	}
+	vips_image_init_fields( out, (int) w, (int) h, 4, VIPS_FORMAT_UCHAR,
+		VIPS_CODING_NONE, VIPS_INTERPRETATION_RGB, 1.0, 1.0 );
+	return( 0 );
+}
+
+static int
+fill_region( VipsRegion *out, void *seq, void *_osr, void *unused,
+	gboolean *stop )
+{
+	openslide_t *osr = _osr;
+	uint32_t *buf;
+	const char *error;
+	PEL *pel;
+	uint32_t sample;
+	uint8_t a;
+	int x, y;
+
+	buf = vips_malloc( NULL, out->valid.width * out->valid.height *
+		sizeof( *buf ));
+	openslide_read_region( osr, buf, out->valid.left, out->valid.top,
+		0, out->valid.width, out->valid.height );
+	for( y = 0; y < out->valid.height; y++ ) {
+		for( x = 0; x < out->valid.width; x++ ) {
+			/* Convert from ARGB to RGBA and undo
+			 * premultiplication.
+			 */
+			sample = buf[y * out->valid.height + x];
+			a = sample >> 24;
+			if( a == 0 ) {
+				/* R, G, B should also be zero, so we just
+				 * need to avoid the zero divide.
+				 */
+				a = 1;
+			}
+			pel = VIPS_REGION_ADDR( out, out->valid.left + x,
+				out->valid.top + y );
+			pel[0] = 255 * ((sample >> 16) & 255) / a;
+			pel[1] = 255 * ((sample >> 8) & 255) / a;
+			pel[2] = 255 * (sample & 255) / a;
+			pel[3] = a;
+		}
+	}
+	vips_free( buf );
+
+	error = openslide_get_error( osr );
+	if( error ) {
+		vips_error( "im_openslide2vips", _( "reading region: %s" ),
+			error );
+		/* OpenSlide handle is now in error state.
+		 */
+		*stop = TRUE;
+		return( -1 );
+	}
+	return( 0 );
+}
+
+static int
+openslide2vips_header( const char *filename, VipsImage *out )
+{
+	openslide_t *osr;
+	int ret;
+
+	osr = openslide_open( filename );
+	if( osr == NULL ) {
+		vips_error( "im_openslide2vips", _( "failure opening slide" ));
+		return( -1 );
+	}
+	ret = load_header( osr, out );
+	openslide_close( osr );
+	return( ret );
+}
+
+/**
+ * im_openslide2vips:
+ * @filename: file to load
+ * @out: image to write to
+ *
+ * Read a virtual slide supported by the OpenSlide library into a VIPS image.
+ * OpenSlide supports images in Aperio, Hamamatsu VMS, Hamamatsu VMU, MIRAX,
+ * and Trestle formats.  It also supports generic tiled TIFF images, but
+ * im_openslide2vips() does not.
+ *
+ * Currently, only layer 0 (the highest-resolution slide layer) is used.
+ *
+ * See also: #VipsFormat
+ *
+ * Returns: 0 on success, -1 on error.
+ */
+static int
+im_openslide2vips( const char *filename, VipsImage *out )
+{
+	openslide_t *osr;
+
+	osr = openslide_open( filename );
+	if( osr == NULL ) {
+		vips_error( "im_openslide2vips", _( "failure opening slide" ));
+		return( -1 );
+	}
+	g_signal_connect( out, "close", G_CALLBACK( close_slide ), osr );
+
+	if( load_header( osr, out ) || vips_image_pio_output( out ))
+		return( -1 );
+	vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
+	return vips_image_generate( out, NULL, fill_region, NULL, osr, NULL );
+}
+
+static int
+isslide( const char *filename )
+{
+	openslide_t *osr;
+	const char *vendor;
+	int ok;
+
+	ok = 1;
+	osr = openslide_open(filename);
+	if( osr != NULL ) {
+		/* If this is a generic tiled TIFF image, decline to support
+		 * it, since im_tiff2vips can do better.
+		 */
+		vendor = openslide_get_property_value( osr,
+			OPENSLIDE_PROPERTY_NAME_VENDOR );
+		if( vendor == NULL ||
+			strcmp( vendor, "generic-tiff" ) == 0 )
+			ok = 0;
+		openslide_close( osr );
+	} else {
+		ok = 0;
+	}
+	return( ok );
+}
+
+static VipsFormatFlags
+slide_flags( const char *filename )
+{
+	return( VIPS_FORMAT_PARTIAL );
+}
+
+/* openslide format adds no new members.
+ */
+typedef VipsFormat VipsFormatOpenslide;
+typedef VipsFormatClass VipsFormatOpenslideClass;
+
+static const char *slide_suffs[] = {
+	".svs",			/* Aperio */
+	".vms", ".vmu",		/* Hamamatsu */
+	".mrxs",		/* MIRAX */
+	".tif",			/* Trestle */
+	NULL
+};
+
+static void
+vips_format_openslide_class_init( VipsFormatOpenslideClass *class )
+{
+	VipsObjectClass *object_class = (VipsObjectClass *) class;
+	VipsFormatClass *format_class = (VipsFormatClass *) class;
+
+	object_class->nickname = "openslide";
+	object_class->description = _( "OpenSlide-supported" );
+
+	format_class->is_a = isslide;
+	format_class->header = openslide2vips_header;
+	format_class->load = im_openslide2vips;
+	format_class->get_flags = slide_flags;
+	format_class->suffs = slide_suffs;
+
+	/* Some TIFF files are virtual slides with odd vendor extensions
+	 * (or outright format violations!).  Ensure we look at them before
+	 * im_tiff2vips does.  OpenSlide tries very hard to reject files it
+	 * doesn't understand, so this should be safe.
+	 */
+	format_class->priority = 100;
+}
+
+static void
+vips_format_openslide_init( VipsFormatOpenslide *object )
+{
+}
+
+G_DEFINE_TYPE( VipsFormatOpenslide, vips_format_openslide, VIPS_TYPE_FORMAT );
+
+#endif /*HAVE_OPENSLIDE*/