Merge remote-tracking branch 'origin/master' into format-hacking

also, start adding openslide.c to foreign

Conflicts:
	ChangeLog
	TODO
	libvips/iofuncs/image.c

ChangeLog

@@ -56,6 +56,7 @@
 - edvips can change vips header byte ordering
 - "header" is terse by default
 - "header" outputs filenames if working on many files
+- added openslide support (Benjamin Gilbert)
 
 12/10/11 started 7.26.6
 - NOCACHE was not being set correctly on OS X causing performance 

README

@@ -140,6 +140,10 @@ OpenEXR
 	if available, libvips will directly read (but not write, sadly)
 	OpenEXR images
 
+OpenSlide
+	if available, libvips can load OpenSlide-supported virtual slide
+	files: Aperio, Hamamatsu VMS and VMU, MIRAX, and Trestle
+
 swig
 python
 python-dev

TODO

@@ -1,9 +1,3 @@
-- do we need vips_object_unref_outputs() in more places? check all calls to
-  _build()
-
-
-
-
 - how about
 
 	vips max add[babe.jpg,babe2.jpg]
@@ -15,6 +9,26 @@
 
 
 
+- add ".ndpi" to openslide suffs? though we don't really use suffs for loaders
+
+- check lazy load hint bug in format-hacking branch
+
+- everywhere must set dhint in header load
+
+- openslide sets a g_log() handler, argh, must just set temp
+
+- make an argb coding type, add to nip2 and known coding
+
+- "background-rgb" should be a macro
+
+- nip2 should use zooming support, if possible
+
+
+
+
+
+
+
 
 - what should we do?
 

configure.in

@@ -438,6 +438,20 @@ if test x"$with_OpenEXR" != "xno"; then
     ])
 fi
 
+# OpenSlide
+AC_ARG_WITH([openslide],
+  AS_HELP_STRING([--without-openslide], [build without OpenSlide (default: test)]))
+
+if test x"$with_openslide" != "xno"; then
+  PKG_CHECK_MODULES(OPENSLIDE, openslide >= 3.2.0,
+    [AC_DEFINE(HAVE_OPENSLIDE,1,[define if you have OpenSlide >= 3.2.0 installed.])
+     with_openslide=yes
+     PACKAGES_USED="$PACKAGES_USED openslide"],
+    [AC_MSG_WARN([OpenSlide >= 3.2.0 not found; disabling virtual slide support])
+     with_openslide=no
+    ])
+fi
+
 # matio
 AC_ARG_WITH([matio], 
   AS_HELP_STRING([--without-matio], [build without matio (default: test)]))
@@ -598,14 +612,14 @@ fi
 # Gather all up for VIPS_CFLAGS, VIPS_INCLUDES, VIPS_LIBS and VIPS_CXX_LIBS
 # sort includes to get longer, more specific dirs first
 # helps, for example, selecting graphicsmagick over imagemagick
-VIPS_CFLAGS=`for i in $VIPS_CFLAGS $GTHREAD_CFLAGS $REQUIRED_CFLAGS $PANGOFT2_CFLAGS $FFTW3_CFLAGS $MAGICK_CFLAGS $PNG_CFLAGS $EXIF_CFLAGS $MATIO_CFLAGS $CFITSIO_CFLAGS $OPENEXR_CFLAGS $ORC_CFLAGS
+VIPS_CFLAGS=`for i in $VIPS_CFLAGS $GTHREAD_CFLAGS $REQUIRED_CFLAGS $PANGOFT2_CFLAGS $FFTW3_CFLAGS $MAGICK_CFLAGS $PNG_CFLAGS $EXIF_CFLAGS $MATIO_CFLAGS $CFITSIO_CFLAGS $OPENEXR_CFLAGS $OPENSLIDE_CFLAGS $ORC_CFLAGS
 do 
   echo $i 
 done | sort -ru`
 VIPS_CFLAGS=`echo $VIPS_CFLAGS`
 VIPS_CFLAGS="$VIPS_DEBUG_FLAGS $VIPS_CFLAGS"
 VIPS_INCLUDES="$PNG_INCLUDES $TIFF_INCLUDES $ZIP_INCLUDES $JPEG_INCLUDES $FFTW_INCLUDES $LCMS_INCLUDES" 
-VIPS_LIBS="$MAGICK_LIBS $PNG_LIBS $TIFF_LIBS $ZIP_LIBS $JPEG_LIBS $GTHREAD_LIBS $REQUIRED_LIBS $PANGOFT2_LIBS $FFTW3_LIBS $FFTW_LIBS $ORC_LIBS $LCMS_LIBS $OPENEXR_LIBS $CFITSIO_LIBS $MATIO_LIBS $EXIF_LIBS -lm"
+VIPS_LIBS="$MAGICK_LIBS $PNG_LIBS $TIFF_LIBS $ZIP_LIBS $JPEG_LIBS $GTHREAD_LIBS $REQUIRED_LIBS $PANGOFT2_LIBS $FFTW3_LIBS $FFTW_LIBS $ORC_LIBS $LCMS_LIBS $OPENEXR_LIBS $OPENSLIDE_LIBS $CFITSIO_LIBS $MATIO_LIBS $EXIF_LIBS -lm"
 
 # we need this to generate paths in swig/python/setup.py.in
 AC_SUBST(top_srcdir)
@@ -682,6 +696,7 @@ accelerate loops with orc: 		$with_orc
   (requires orc-0.4.11 or later)
 ICC profile support with lcms: 		$with_lcms (version $with_lcms_ver)
 file import with OpenEXR: 		$with_OpenEXR
+file import with OpenSlide:		$with_openslide
 file import with matio: 		$with_matio
 file import with cfitsio: 		$with_cfitsio
 text rendering with pangoft2: 		$with_pangoft2

libvips/arithmetic/measure.c

@@ -50,8 +50,8 @@
  */
 
 /*
- */
 #define VIPS_DEBUG
+ */
 
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -159,7 +159,7 @@ vips_measure_build( VipsObject *object )
 				 * measure on IM_TYPE_LAB images).
 				 */
 				if( dev * 5 > fabs( avg ) && fabs( avg ) > 3 )
-					im_warn( "im_measure",
+					vips_warn( "VipsMeasure",
 						_( "patch %d x %d, band %d: " 
 						   "avg = %g, sdev = %g" ), 
 						i, j, avg, dev );

libvips/arithmetic/stats.c

@@ -56,8 +56,8 @@
  */
 
 /*
- */
 #define VIPS_DEBUG
+ */
 
 #ifdef HAVE_CONFIG_H
 #include <config.h>

libvips/colour/Makefile.am

@@ -6,6 +6,7 @@ libcolour_la_SOURCES = \
 	colour_dispatch.c \
 	derived.c \
 	im_icc_transform.c \
+	im_argb2rgba.c \
 	im_LCh2Lab.c \
 	im_LCh2UCS.c \
 	im_Lab2LCh.c \

libvips/colour/colour_dispatch.c

@@ -640,6 +640,25 @@ static im_function rad2float_desc = {
 	one_in_one_out 			/* Arg list */
 };
 
+/* Call im_argb2rgba() via arg vector.
+ */
+static int
+argb2rgba_vec( im_object *argv )
+{
+	return( im_argb2rgba( argv[0], argv[1] ) );
+}
+
+/* Description of im_argb2rgba.
+ */ 
+static im_function argb2rgba_desc = {
+	"im_argb2rgba", 		/* Name */
+	"convert pre-multipled argb to png-style rgba",	/* Description */
+	IM_FN_PIO,			/* Flags */
+	argb2rgba_vec, 			/* Dispatch function */
+	IM_NUMBER( one_in_one_out ), 	/* Size of arg list */
+	one_in_one_out 			/* Arg list */
+};
+
 /* Call im_float2rad() via arg vector.
  */
 static int
@@ -1185,6 +1204,7 @@ static im_function *colour_list[] = {
 	&disp2Lab_desc,
 	&disp2XYZ_desc,
 	&float2rad_desc,
+	&argb2rgba_desc,
 	&icc_ac2rc_desc,
 	&icc_export_depth_desc,
 	&icc_import_desc,

libvips/colour/im_argb2rgba.c

@@ -0,0 +1,110 @@
+/* Convert pre-multipled argb to rgba
+ *
+ * 11/12/11
+ * 	- from im_rad2float.c
+ */
+
+/*
+
+    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
+
+ */
+
+/*
+
+    These files are distributed with VIPS - http://www.vips.ecs.soton.ac.uk
+
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif /*HAVE_CONFIG_H*/
+#include <vips/intl.h>
+
+#include <stdio.h>
+#include <math.h>
+
+#include <vips/vips.h>
+
+static void
+argb2rgba( guint32 *in, PEL *out, int n, void *_bg )
+{
+	guint32 bg = GPOINTER_TO_UINT( _bg );
+
+	int i;
+
+	for( i = 0; i < n; i++ ) {
+		guint32 x = in[i];
+		guint8 a = x >> 24;
+
+		/* Convert from ARGB to RGBA and undo premultiplication.
+		 */
+		if( a != 0 ) {
+			out[0] = 255 * ((x >> 16) & 255) / a;
+			out[1] = 255 * ((x >> 8) & 255) / a;
+			out[2] = 255 * (x & 255) / a;
+		} 
+		else {
+			/* Use background color.
+			 */
+			out[0] = (bg >> 16) & 255;
+			out[1] = (bg >> 8) & 255;
+			out[2] = bg & 255;
+		}
+		out[3] = a;
+
+		out += 4;
+	}
+}
+
+/**
+ * im_argb2rgba:
+ * @in: input image
+ * @out: output image
+ *
+ * Convert Cairo-style pre-multiplied argb to png-style rgba. Background
+ * pixels are painted with the metadata item "background-rgb".
+ *
+ * See also: im_openslide2vips().
+ *
+ * Returns: 0 on success, -1 on error.
+ */
+int
+im_argb2rgba( IMAGE *in, IMAGE *out )
+{
+	guint32 bg;
+
+	/* check for RAD coding 
+	if( in->Coding != IM_CODING_RAD ) {
+		im_error( "im_rad2float", "%s", _( "not a RAD image" ) );
+		return( -1 );
+	}
+	 */
+
+	if( im_cp_desc( out, in ) )
+		return( -1 );
+	out->Coding = IM_CODING_NONE;
+
+	if( im_meta_get_int( in, "background-rgb", (int *) &bg ) )
+		bg = 0xffffff;
+
+	if( im_wrapone( in, out, 
+		(im_wrapone_fn) argb2rgba, GUINT_TO_POINTER( bg ), NULL ) )
+		return( -1 );
+
+	return( 0 );
+}

libvips/conversion/flip.c

@@ -133,7 +133,7 @@ vips_flip_horizontal_gen( VipsRegion *or, void *seq, void *a, void *b,
 	VipsRegion *ir = (VipsRegion *) seq;
 	VipsRect *r = &or->valid;
 	VipsRect in;
-	char *p, *q;
+	PEL *p, *q;
 	int x, y, z;
 
 	int le = r->left;

libvips/conversion/im_subsample.c

@@ -85,8 +85,8 @@ line_shrink_gen( REGION *or, void *seq, void *a, void *b )
 	/* Loop down the region.
 	 */
 	for( y = to; y < bo; y++ ) {
-		char *q = IM_REGION_ADDR( or, le, y );
+		PEL *q = IM_REGION_ADDR( or, le, y );
-		char *p;
+		PEL *p;
 
 		/* Loop across the region, in owidth sized pieces.
 		 */
@@ -149,8 +149,8 @@ point_shrink_gen( REGION *or, void *seq, void *a, void *b )
 	/* Loop down the region.
 	 */
 	for( y = to; y < bo; y++ ) {
-		char *q = IM_REGION_ADDR( or, le, y );
+		PEL *q = IM_REGION_ADDR( or, le, y );
-		char *p;
+		PEL *p;
 
 		/* Loop across the region, in owidth sized pieces.
 		 */

libvips/foreign/openslide.c

@@ -0,0 +1,377 @@
+/* Read a virtual microscope slide using OpenSlide.
+ *
+ * Benjamin Gilbert
+ *
+ * Copyright (c) 2011 Carnegie Mellon University
+ *
+ * 26/11/11
+ *	- initial version
+ * 27/11/11
+ *	- fix black background in transparent areas
+ *	- no need to set *stop on fill_region() error return
+ *	- add OpenSlide properties to image metadata
+ *	- consolidate setup into one function
+ *	- support reading arbitrary layers
+ *	- use VIPS_ARRAY()
+ *	- add helper to copy a line of pixels
+ *	- support reading associated images
+ * 7/12/11
+ *	- redirect OpenSlide error logging to vips_error()
+ * 8/12/11
+ *	- add more exposition to documentation
+ * 9/12/11
+ * 	- unpack to a tile cache
+ * 11/12/11
+ * 	- move argb->rgba into conversion
+ * 	- turn into a set of read fns ready to be called from a class
+ */
+
+/*
+
+    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
+
+ */
+
+/*
+#define VIPS_DEBUG
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif /*HAVE_CONFIG_H*/
+#include <vips/intl.h>
+
+#include <string.h>
+#include <stdint.h>
+#include <stdlib.h>
+#include <limits.h>
+
+#include <vips/vips.h>
+#include <vips/debug.h>
+
+#include <openslide.h>
+
+#include "openslide.h"
+
+/* We run our own tile cache. The OpenSlide one can't always keep enough for a
+ * complete lines of pixels.
+ */
+#define TILE_WIDTH (256)
+#define TILE_HEIGHT (256)
+
+typedef struct {
+	openslide_t *osr;
+	const char *associated;
+
+	/* Only valid if associated == NULL.
+	 */
+	int32_t layer;
+	double downsample;
+} ReadSlide;
+
+int
+vips__openslide_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;
+
+	VIPS_DEBUG_MSG( "vips__openslide_isslide: %s - %d\n", filename, ok );
+
+	return( ok );
+}
+
+static void
+readslide_destroy_cb( VipsImage *image, ReadSlide *rslide )
+{
+	VIPS_FREEF( openslide_close, rslide->osr );
+}
+
+static int
+check_associated_image( openslide_t *osr, const char *name )
+{
+	const char * const *associated;
+
+	for( associated = openslide_get_associated_image_names( osr );
+		*associated != NULL; associated++ )
+		if( strcmp( *associated, name ) == 0 )
+			return( 0 );
+
+	vips_error( "im_openslide2vips", 
+		"%s", _( "invalid associated image name" ) );
+
+	return( -1 );
+}
+
+static ReadSlide *
+readslide_new( const char *filename, VipsImage *out )
+{
+	ReadSlide *rslide;
+	char name[FILENAME_MAX];
+	char mode[FILENAME_MAX];
+	char *endp;
+	int64_t w, h;
+	const char *background;
+	const char * const *properties;
+	char *associated;
+
+	rslide = VIPS_NEW( out, ReadSlide );
+	memset( rslide, 0, sizeof( *rslide ) );
+	g_signal_connect( out, "close", G_CALLBACK( readslide_destroy_cb ),
+		rslide );
+
+	vips_filename_split( filename, name, mode );
+	rslide->osr = openslide_open( name );
+	if( rslide->osr == NULL ) {
+		vips_error( "im_openslide2vips", 
+			"%s", _( "failure opening slide" ) );
+		return( NULL );
+	}
+
+	/* Parse optional mode.
+	 */
+	rslide->layer = strtol( mode, &endp, 10 );
+	if( *mode != 0 && *endp == 0 ) {
+		/* Mode specifies slide layer.
+		 */
+		if( rslide->layer < 0 || rslide->layer >=
+			openslide_get_layer_count( rslide->osr ) ) {
+			vips_error( "im_openslide2vips",
+				"%s", _( "invalid slide layer" ) );
+			return( NULL );
+		}
+	} 
+	else if( *mode != 0 ) {
+		/* Mode specifies associated image.
+		 */
+		if ( check_associated_image( rslide->osr, mode ) )
+			return( NULL );
+		rslide->associated = vips_strdup( VIPS_OBJECT( out ), mode );
+	}
+
+	if( rslide->associated ) {
+		openslide_get_associated_image_dimensions( rslide->osr,
+			rslide->associated, &w, &h );
+		vips_image_set_string( out, "slide-associated-image",
+			rslide->associated );
+		vips_demand_hint( out, VIPS_DEMAND_STYLE_THINSTRIP, NULL );
+	} 
+	else {
+		openslide_get_layer_dimensions( rslide->osr, rslide->layer,
+			&w, &h );
+		rslide->downsample = openslide_get_layer_downsample(
+			rslide->osr, rslide->layer );
+		vips_image_set_int( out, "slide-layer", rslide->layer );
+		vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
+	}
+
+	/* This tag is used by argb2rgba() to paint fully-transparent pixels.
+	 */
+	background = openslide_get_property_value( rslide->osr,
+		OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR );
+	if( background != NULL )
+		im_meta_set_int( out, 
+			"background-rgb", strtoul( background, NULL, 16 ) );
+	else
+		im_meta_set_int( out, "background-rgb", 0xffffff );
+
+	if( w < 0 || h < 0 || rslide->downsample < 0 ) {
+		vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
+			openslide_get_error( rslide->osr ) );
+		return( NULL );
+	}
+	if( w > INT_MAX || 
+		h > INT_MAX ) {
+		vips_error( "im_openslide2vips",
+			"%s", _( "image dimensions overflow int" ) );
+		return( NULL );
+	}
+
+	vips_image_init_fields( out, (int) w, (int) h, 4, VIPS_FORMAT_UCHAR,
+		VIPS_CODING_NONE, VIPS_INTERPRETATION_RGB, 1.0, 1.0 );
+
+	for( properties = openslide_get_property_names( rslide->osr );
+		*properties != NULL; properties++ )
+		vips_image_set_string( out, *properties,
+			openslide_get_property_value( rslide->osr,
+			*properties ) );
+
+	associated = g_strjoinv( ", ", (char **)
+		openslide_get_associated_image_names( rslide->osr ) );
+	vips_image_set_string( out, "slide-associated-images", associated );
+	g_free( associated );
+
+	return( rslide );
+}
+
+int
+vips__openslide_read_header( const char *filename, VipsImage *out, 
+	int layer, char *associated )
+{
+	ReadSlide *rslide;
+
+	if( !(rslide = readslide_new( filename, out, layer, associated )) )
+		return( -1 );
+
+	return( 0 );
+}
+
+static int
+fill_region( VipsRegion *out, void *seq, void *_rslide, void *unused,
+	gboolean *stop )
+{
+	ReadSlide *rslide = _rslide;
+	VipsRect *r = &out->valid;
+
+	const char *error;
+	int x, y;
+
+	VIPS_DEBUG_MSG( "fill_region: %dx%d @ %dx%d\n",
+		r->width, r->height, r->left, r->top );
+
+	/* Fill in tile-sized chunks. Some versions of OpenSlide can fail for
+	 * very large dimensions.
+	 */
+	for( y = 0; y < r->height; y += TILE_HEIGHT ) 
+		for( x = 0; x < r->width; x += TILE_WIDTH ) {
+			int w = VIPS_MIN( TILE_WIDTH, r->width - x );
+			int h = VIPS_MIN( TILE_HEIGHT, r->height - y );
+
+			openslide_read_region( rslide->osr, 
+				(uint32_t *) VIPS_REGION_ADDR( out, 
+					r->left + x, r->top + y ),
+				(r->left + x) * rslide->downsample, 
+				(r->top + y) * rslide->downsample, 
+				rslide->layer,
+				w, h ); 
+		}
+
+	error = openslide_get_error( rslide->osr );
+	if( error ) {
+		vips_error( "im_openslide2vips", 
+			_( "reading region: %s" ), error );
+
+		return( -1 );
+	}
+
+	return( 0 );
+}
+
+int
+vips__openslide_read_file( const char *filename, VipsImage *out, int layer )
+{
+	ReadSlide *rslide;
+	VipsImage *raw;
+
+	VIPS_DEBUG_MSG( "vips__openslide_read_file: %s %d\n", 
+		filename, layer );
+
+	/* Tile cache: keep enough for two complete rows of tiles.
+	 * This lets us do (smallish) area ops, like im_conv(), while
+	 * still only hitting each tile once.
+	 */
+	if( !(raw = im_open_local( out, "cache", "p" )) )
+		return( -1 );
+
+	if( !(rslide = readslide_new( filename, raw, layer, NULL )) )
+		return( -1 );
+
+	if( vips_image_pio_output( raw ) ||
+		vips_image_generate( raw, 
+			NULL, fill_region, NULL, rslide, NULL ) )
+		return( -1 );
+
+	/* Copy to out, adding a cache. Enough tiles for a complete row, plus
+	 * 50%.
+	 */
+	if( im_tile_cache( raw, out, 
+		TILE_WIDTH, TILE_HEIGHT,
+		1.5 * (1 + raw->Xsize / TILE_WIDTH) ) ) 
+		return( -1 );
+
+	return( 0 );
+}
+
+int
+vips__openslide_read_associated( const char *filename, VipsImage *out, 
+	const char *associated )
+{
+	ReadSlide *rslide;
+	VipsImage *raw;
+	uint32_t *buf;
+	int64_t w, h;
+	int y;
+	const char *error;
+
+	VIPS_DEBUG_MSG( "vips__openslide_read_associated: %s %s\n", 
+		filename, associated );
+
+	/* Tile cache: keep enough for two complete rows of tiles.
+	 * This lets us do (smallish) area ops, like im_conv(), while
+	 * still only hitting each tile once.
+	 */
+	if( !(raw = im_open_local( out, "cache", "p" )) )
+		return( -1 );
+
+	if( !(rslide = readslide_new( filename, raw, 0, associated )) )
+		return( -1 );
+
+	openslide_get_associated_image_dimensions( rslide->osr,
+		rslide->associated, &w, &h );
+	if( w == -1 || 
+		h == -1 ) {
+		vips_error( "im_openslide2vips", 
+			_( "getting dimensions: %s" ),
+			openslide_get_error( rslide->osr ) );
+
+		return( -1 );
+	}
+
+	buf = VIPS_ARRAY( out, w * h, uint32_t );
+	openslide_read_associated_image( rslide->osr, rslide->associated, buf );
+	error = openslide_get_error( rslide->osr );
+	if( error ) {
+		vips_error( "im_openslide2vips",
+			_( "reading associated image: %s" ), error );
+		return( -1 );
+	}
+
+	if( vips_image_wio_output( out ) )
+		return( -1 );
+	for( y = 0; y < h; y++ ) 
+		if( vips_image_write_line( out, y, (PEL *) (buf + y * w) ) )
+			return( -1 );
+
+	return( 0 );
+}
+

libvips/foreign/openslide.h

@@ -0,0 +1,47 @@
+/* common defs for jpeg read/write
+ */
+
+/*
+
+    Copyright (C) 1991-2005 The National Gallery
+
+    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
+
+ */
+
+/*
+
+    These files are distributed with VIPS - http://www.vips.ecs.soton.ac.uk
+
+ */
+
+#ifndef VIPS_OPENSLIDE_H
+#define VIPS_OPENSLIDE_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif /*__cplusplus*/
+
+int vips__openslide_isslide( const char *filename );
+int vips__openslide_read_header( const char *filename, VipsImage *out );
+int vips__openslide_read_file( const char *filename, VipsImage *out );
+int vips__openslide_read_associated( const char *filename, VipsImage *out, 
+	const char *associated );
+
+#ifdef __cplusplus
+}
+#endif /*__cplusplus*/
+
+#endif /*VIPS_OPENSLIDE_H*/

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

@@ -57,7 +57,7 @@
  * transparently supported by im_open().
  *
  * VIPS comes with VipsFormat for TIFF, JPEG, PNG, Analyze, PPM, OpenEXR, CSV,
- * Matlab, Radiance, RAW, VIPS and one that wraps libMagick. 
+ * Matlab, Radiance, RAW, VIPS and ones that wrap libMagick and OpenSlide.
  */
 
 /**
@@ -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 +1,469 @@
+/* Read a virtual microscope slide using OpenSlide.
+ *
+ * Benjamin Gilbert
+ *
+ * Copyright (c) 2011 Carnegie Mellon University
+ *
+ * 26/11/11
+ *	- initial version
+ * 27/11/11
+ *	- fix black background in transparent areas
+ *	- no need to set *stop on fill_region() error return
+ *	- add OpenSlide properties to image metadata
+ *	- consolidate setup into one function
+ *	- support reading arbitrary layers
+ *	- use VIPS_ARRAY()
+ *	- add helper to copy a line of pixels
+ *	- support reading associated images
+ * 7/12/11
+ *	- redirect OpenSlide error logging to vips_error()
+ * 8/12/11
+ *	- add more exposition to documentation
+ * 9/12/11
+ * 	- unpack to a tile cache
+ * 11/12/11
+ * 	- move argb->rgba into conversion
+ */
+
+/*
+
+    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
+
+ */
+
+/*
+#define VIPS_DEBUG
+ */
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif /*HAVE_CONFIG_H*/
+#include <vips/intl.h>
+
+#ifdef HAVE_OPENSLIDE
+
+#include <string.h>
+#include <stdint.h>
+#include <stdlib.h>
+#include <limits.h>
+
+#include <vips/vips.h>
+#include <vips/debug.h>
+
+#include <openslide.h>
+
+/* We run our own tile cache. The OpenSlide one can't always keep enough for a
+ * complete lines of pixels.
+ */
+#define TILE_WIDTH (256)
+#define TILE_HEIGHT (256)
+
+typedef struct {
+	openslide_t *osr;
+	const char *associated;
+
+	/* Only valid if associated == NULL.
+	 */
+	int32_t layer;
+	double downsample;
+} ReadSlide;
+
+static void
+readslide_destroy_cb( VipsImage *image, ReadSlide *rslide )
+{
+	VIPS_FREEF( openslide_close, rslide->osr );
+}
+
+static int
+check_associated_image( openslide_t *osr, const char *name )
+{
+	const char * const *associated;
+
+	for( associated = openslide_get_associated_image_names( osr );
+		*associated != NULL; associated++ )
+		if( strcmp( *associated, name ) == 0 )
+			return( 0 );
+
+	vips_error( "im_openslide2vips", 
+		"%s", _( "invalid associated image name" ) );
+
+	return( -1 );
+}
+
+static ReadSlide *
+readslide_new( const char *filename, VipsImage *out )
+{
+	ReadSlide *rslide;
+	char name[FILENAME_MAX];
+	char mode[FILENAME_MAX];
+	char *endp;
+	int64_t w, h;
+	const char *background;
+	const char * const *properties;
+	char *associated;
+
+	rslide = VIPS_NEW( out, ReadSlide );
+	memset( rslide, 0, sizeof( *rslide ) );
+	g_signal_connect( out, "close", G_CALLBACK( readslide_destroy_cb ),
+		rslide );
+
+	vips_filename_split( filename, name, mode );
+	rslide->osr = openslide_open( name );
+	if( rslide->osr == NULL ) {
+		vips_error( "im_openslide2vips", 
+			"%s", _( "failure opening slide" ) );
+		return( NULL );
+	}
+
+	/* Parse optional mode.
+	 */
+	rslide->layer = strtol( mode, &endp, 10 );
+	if( *mode != 0 && *endp == 0 ) {
+		/* Mode specifies slide layer.
+		 */
+		if( rslide->layer < 0 || rslide->layer >=
+			openslide_get_layer_count( rslide->osr ) ) {
+			vips_error( "im_openslide2vips",
+				"%s", _( "invalid slide layer" ) );
+			return( NULL );
+		}
+	} 
+	else if( *mode != 0 ) {
+		/* Mode specifies associated image.
+		 */
+		if ( check_associated_image( rslide->osr, mode ) )
+			return( NULL );
+		rslide->associated = vips_strdup( VIPS_OBJECT( out ), mode );
+	}
+
+	if( rslide->associated ) {
+		openslide_get_associated_image_dimensions( rslide->osr,
+			rslide->associated, &w, &h );
+		vips_image_set_string( out, "slide-associated-image",
+			rslide->associated );
+		vips_demand_hint( out, VIPS_DEMAND_STYLE_THINSTRIP, NULL );
+	} 
+	else {
+		openslide_get_layer_dimensions( rslide->osr, rslide->layer,
+			&w, &h );
+		rslide->downsample = openslide_get_layer_downsample(
+			rslide->osr, rslide->layer );
+		vips_image_set_int( out, "slide-layer", rslide->layer );
+		vips_demand_hint( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
+	}
+
+	/* This tag is used by argb2rgba() to paint fully-transparent pixels.
+	 */
+	background = openslide_get_property_value( rslide->osr,
+		OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR );
+	if( background != NULL )
+		im_meta_set_int( out, 
+			"background-rgb", strtoul( background, NULL, 16 ) );
+	else
+		im_meta_set_int( out, "background-rgb", 0xffffff );
+
+	if( w < 0 || h < 0 || rslide->downsample < 0 ) {
+		vips_error( "im_openslide2vips", _( "getting dimensions: %s" ),
+			openslide_get_error( rslide->osr ) );
+		return( NULL );
+	}
+	if( w > INT_MAX || 
+		h > INT_MAX ) {
+		vips_error( "im_openslide2vips",
+			"%s", _( "image dimensions overflow int" ) );
+		return( NULL );
+	}
+
+	vips_image_init_fields( out, (int) w, (int) h, 4, VIPS_FORMAT_UCHAR,
+		VIPS_CODING_NONE, VIPS_INTERPRETATION_RGB, 1.0, 1.0 );
+
+	for( properties = openslide_get_property_names( rslide->osr );
+		*properties != NULL; properties++ )
+		vips_image_set_string( out, *properties,
+			openslide_get_property_value( rslide->osr,
+			*properties ) );
+
+	associated = g_strjoinv( ", ", (char **)
+		openslide_get_associated_image_names( rslide->osr ) );
+	vips_image_set_string( out, "slide-associated-images", associated );
+	g_free( associated );
+
+	return( rslide );
+}
+
+static int
+fill_region( VipsRegion *out, void *seq, void *_rslide, void *unused,
+	gboolean *stop )
+{
+	ReadSlide *rslide = _rslide;
+	VipsRect *r = &out->valid;
+
+	const char *error;
+	int x, y;
+
+	VIPS_DEBUG_MSG( "fill_region: %dx%d @ %dx%d\n",
+		r->width, r->height, r->left, r->top );
+
+	/* Fill in tile-sized chunks. Some versions of OpenSlide can fail for
+	 * very large dimensions.
+	 */
+	for( y = 0; y < r->height; y += TILE_HEIGHT ) 
+		for( x = 0; x < r->width; x += TILE_WIDTH ) {
+			int w = VIPS_MIN( TILE_WIDTH, r->width - x );
+			int h = VIPS_MIN( TILE_HEIGHT, r->height - y );
+
+			openslide_read_region( rslide->osr, 
+				(uint32_t *) VIPS_REGION_ADDR( out, 
+					r->left + x, r->top + y ),
+				(r->left + x) * rslide->downsample, 
+				(r->top + y) * rslide->downsample, 
+				rslide->layer,
+				w, h ); 
+		}
+
+	error = openslide_get_error( rslide->osr );
+	if( error ) {
+		vips_error( "im_openslide2vips", 
+			_( "reading region: %s" ), error );
+
+		return( -1 );
+	}
+
+	return( 0 );
+}
+
+static int
+fill_associated( VipsImage *out, ReadSlide *rslide )
+{
+	uint32_t *buf;
+	int64_t w, h;
+	int y;
+	const char *error;
+
+	openslide_get_associated_image_dimensions( rslide->osr,
+		rslide->associated, &w, &h );
+	if( w == -1 || 
+		h == -1 ) {
+		vips_error( "im_openslide2vips", 
+			_( "getting dimensions: %s" ),
+			openslide_get_error( rslide->osr ) );
+
+		return( -1 );
+	}
+
+	buf = VIPS_ARRAY( out, w * h, uint32_t );
+	openslide_read_associated_image( rslide->osr, rslide->associated, buf );
+	error = openslide_get_error( rslide->osr );
+	if( error ) {
+		vips_error( "im_openslide2vips",
+			_( "reading associated image: %s" ), error );
+		return( -1 );
+	}
+
+	if( vips_image_wio_output( out ) )
+		return( -1 );
+	for( y = 0; y < h; y++ ) 
+		if( vips_image_write_line( out, y, (PEL *) (buf + y * w) ) )
+			return( -1 );
+
+	return( 0 );
+}
+
+static int
+openslide2vips_header( const char *filename, VipsImage *out )
+{
+	ReadSlide *rslide;
+
+	if( !(rslide = readslide_new( filename, out )) )
+		return( -1 );
+
+	return( 0 );
+}
+
+/**
+ * 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.
+ *
+ * To facilitate zooming, virtual slide formats include multiple scaled-down
+ * versions of the high-resolution image.  These are typically called
+ * "levels", though OpenSlide and im_openslide2vips() call them "layers".
+ * By default, im_openslide2vips() reads the highest-resolution layer
+ * (layer 0).  To read a different layer, specify the layer number as part
+ * of the filename (for example, "CMU-1.mrxs:3").
+ *
+ * In addition to the slide image itself, virtual slide formats sometimes
+ * include additional images, such as a scan of the slide's barcode.
+ * OpenSlide calls these "associated images".  To read an associated image,
+ * specify the image's name as part of the filename (for example,
+ * "CMU-1.mrxs:label").  A slide's associated images are listed in the
+ * "slide-associated-images" metadata item.
+ *
+ * See also: #VipsFormat
+ *
+ * Returns: 0 on success, -1 on error.
+ */
+static int
+im_openslide2vips( const char *filename, VipsImage *out )
+{
+	ReadSlide *rslide;
+	VipsImage *raw;
+
+	VIPS_DEBUG_MSG( "im_openslide2vips: %s\n", filename );
+
+	/* Tile cache: keep enough for two complete rows of tiles.
+	 * This lets us do (smallish) area ops, like im_conv(), while
+	 * still only hitting each tile once.
+	 */
+	if( !(raw = im_open_local( out, "cache", "p" )) )
+		return( -1 );
+
+	if( !(rslide = readslide_new( filename, raw )) )
+		return( -1 );
+
+	if( rslide->associated ) {
+		VIPS_DEBUG_MSG( "fill_associated:\n" );
+
+		if( fill_associated( raw, rslide ) )
+			return( -1 );
+	} 
+	else {
+		if( vips_image_pio_output( raw ) ||
+			vips_image_generate( raw, 
+				NULL, fill_region, NULL, rslide, NULL ) )
+			return( -1 );
+	}
+
+	/* Copy to out, adding a cache. Enough tiles for two complete 
+	 * rows.
+	 */
+	if( im_tile_cache( raw, out, 
+		TILE_WIDTH, TILE_HEIGHT,
+		2 * (1 + raw->Xsize / TILE_WIDTH) ) ) 
+		return( -1 );
+
+	return( 0 );
+}
+
+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;
+
+	VIPS_DEBUG_MSG( "isslide: %s - %d\n", filename, ok );
+
+	return( ok );
+}
+
+static VipsFormatFlags
+slide_flags( const char *filename )
+{
+	char name[FILENAME_MAX];
+	char mode[FILENAME_MAX];
+	char *endp;
+
+	vips_filename_split( filename, name, mode );
+	strtol( mode, &endp, 10 );
+	if( *mode == 0 || 
+		*endp == 0 ) 
+		/* Slide layer or no mode specified.
+		 */
+		return( VIPS_FORMAT_PARTIAL );
+	else 
+		/* Associated image specified.
+		 */
+		return( 0 );
+}
+
+static void
+error_handler( const char *domain, GLogLevelFlags level, const char *message,
+	void *data )
+{
+	vips_error( "im_openslide2vips", "%s", message );
+}
+
+/* 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;
+
+	g_log_set_handler( "Openslide",
+		G_LOG_LEVEL_CRITICAL | G_LOG_LEVEL_WARNING,
+		error_handler, NULL );
+}
+
+static void
+vips_format_openslide_init( VipsFormatOpenslide *object )
+{
+}
+
+G_DEFINE_TYPE( VipsFormatOpenslide, vips_format_openslide, VIPS_TYPE_FORMAT );
+
+#endif /*HAVE_OPENSLIDE*/

libvips/histograms_lut/im_histnD.c

@@ -171,7 +171,7 @@ find_hist( REGION *reg, void *seq, void *a, void *b, gboolean *stop )
 	/* Accumulate!
 	 */
 	for( y = to; y < bo; y++ ) {
-		char *line = IM_REGION_ADDR( reg, le, y );
+		PEL *line = IM_REGION_ADDR( reg, le, y );
 
 		switch( im->BandFmt ) {
 		case IM_BANDFMT_UCHAR:

libvips/include/vips/colour.h

@@ -142,6 +142,7 @@ float im_col_dE00(
 int im_LCh2Lab( VipsImage *in, VipsImage *out );
 int im_LabQ2XYZ( VipsImage *in, VipsImage *out );
 int im_rad2float( VipsImage *in, VipsImage *out );
+int im_argb2rgba( VipsImage *in, VipsImage *out );
 int im_float2rad( VipsImage *in, VipsImage *out );
 int im_LCh2UCS( VipsImage *in, VipsImage *out );
 int im_Lab2LCh( VipsImage *in, VipsImage *out );

libvips/include/vips/header.h

@@ -77,7 +77,7 @@ extern "C" {
  */
 #define VIPS_META_RESOLUTION_UNIT "resolution-unit"
 
-int vips_format_sizeof( VipsBandFormat format );
+guint64 vips_format_sizeof( VipsBandFormat format );
 
 int vips_image_get_width( const VipsImage *image );
 int vips_image_get_height( const VipsImage *image );

libvips/include/vips/image.h

@@ -282,7 +282,7 @@ typedef struct _VipsImage {
 	 */
 	char *Hist;		/* don't use, see vips_image_get_history() */
 	char *filename;		/* pointer to copy of filename */
-	char *data;		/* start of image data for WIO */
+	PEL *data;		/* start of image data for WIO */
 	int kill;		/* set to non-zero to block eval */
 
 	/* Everything below this private and only used internally by
@@ -292,7 +292,7 @@ typedef struct _VipsImage {
 	char *mode;		/* mode string passed to _new() */
 	VipsImageType dtype;	/* descriptor type */
 	int fd;         	/* file descriptor */
-	char *baseaddr;     	/* pointer to the start of an mmap file */
+	void *baseaddr;     	/* pointer to the start of an mmap file */
 	size_t length;		/* size of mmap area */
 	guint32 magic;		/* magic from header, endian-ness of image */
 
@@ -316,8 +316,11 @@ typedef struct _VipsImage {
 	/* Part of mmap() read ... the sizeof() the header we skip from the
 	 * file start. Usually VIPS_SIZEOF_HEADER, but can be something else
 	 * for binary file read.
+	 *
+	 * gint64 so that we can guarantee to work even on systems with
+	 * strange ideas about large files.
 	 */
-	int sizeof_header;
+	guint64 sizeof_header;
 
 	/* If this is a large disc image, don't map the whole thing, instead
 	 * have a set of windows shared between the regions active on the
@@ -372,7 +375,6 @@ typedef struct _VipsImage {
 	 */
 	gboolean delete_on_close;
 	char *delete_on_close_filename;
-
 } VipsImage;
 
 typedef struct _VipsImageClass {
@@ -443,7 +445,7 @@ extern const size_t vips__image_sizeof_bandformat[];
 		(X), (Y), \
 		0, 0, \
 		(I)->Xsize, \
-		(I)->Ysize ), abort(), (char *) NULL) \
+		(I)->Ysize ), abort(), (PEL *) NULL) \
 	)
 #else /*!VIPS_DEBUG*/
 #define VIPS_IMAGE_ADDR( I, X, Y ) \
@@ -468,7 +470,7 @@ VipsImage *vips_image_new( void );
 VipsImage *vips_image_new_mode( const char *filename, const char *mode );
 VipsImage *vips_image_new_from_file( const char *filename );
 VipsImage *vips_image_new_from_file_raw( const char *filename, 
-	int xsize, int ysize, int bands, int offset );
+	int xsize, int ysize, int bands, guint64 offset );
 VipsImage *vips_image_new_from_memory( void *buffer, 
 	int xsize, int ysize, int bands, VipsBandFormat bandfmt );
 VipsImage *vips_image_new_array( int xsize, int ysize );

libvips/include/vips/object.h

@@ -168,6 +168,19 @@ extern int _vips__argument_id;
 		pspec, (FLAGS), (PRIORITY), (OFFSET) ); \
 }
 
+#define VIPS_ARG_UINT64( CLASS, NAME, PRIORITY, LONG, DESC, \
+	FLAGS, OFFSET, MIN, MAX, VALUE ) { \
+	GParamSpec *pspec; \
+	\
+	pspec = g_param_spec_uint64( (NAME), (LONG), (DESC), \
+		(MIN), (MAX), (VALUE), \
+		G_PARAM_READWRITE );\
+	g_object_class_install_property( G_OBJECT_CLASS( CLASS ), \
+		_vips__argument_id++, pspec ); \
+	vips_object_class_install_argument( VIPS_OBJECT_CLASS( CLASS ), \
+		pspec, (FLAGS), (PRIORITY), (OFFSET) ); \
+}
+
 #define VIPS_ARG_ENUM( CLASS, NAME, PRIORITY, LONG, DESC, \
 	FLAGS, OFFSET, TYPE, VALUE ) { \
 	GParamSpec *pspec; \

libvips/include/vips/private.h

@@ -66,9 +66,9 @@ typedef struct {
 
 	int top; 		/* Area of image we have mapped, in pixels */
 	int height;
-	char *data;		/* First pixel of line 'top' */
+	PEL *data;		/* First pixel of line 'top' */
 
-	PEL *baseaddr;		/* Base of window */
+	void *baseaddr;		/* Base of window */
 	size_t length;		/* Size of window */
 } VipsWindow;
 
@@ -106,7 +106,7 @@ typedef struct {
 	VipsRect area;		/* Area this pixel buffer covers */
 	gboolean done;		/* Calculated and in cache */
 	VipsBufferCache *cache;
-	char *buf;		/* Private malloc() area */
+	PEL *buf;		/* Private malloc() area */
 	size_t bsize;		/* Size of private malloc() */
 } VipsBuffer;
 

libvips/include/vips/region.h

@@ -69,7 +69,7 @@ typedef struct _VipsRegion {
 	 */
 	/*< private >*/
 	RegionType type;	/* What kind of attachment */
-	char *data;		/* Off here to get data */
+	PEL *data;		/* Off here to get data */
 	int bpl;		/* Bytes-per-line for data */
 	void *seq;		/* Sequence we are using to fill region */
 
@@ -150,7 +150,7 @@ int vips_region_prepare_many( VipsRegion **reg, VipsRect *r );
 		(R)->valid.left, \
 		(R)->valid.top, \
 		(R)->valid.width, \
-		(R)->valid.height ), abort(), (char *) NULL) \
+		(R)->valid.height ), abort(), (PEL *) NULL) \
 	)
 #else /*DEBUG*/
 #define VIPS_REGION_ADDR( R, X, Y ) \

libvips/iofuncs/header.c

@@ -186,8 +186,11 @@ static HeaderField old_double_field[] = {
 
 /* This is used by (eg.) VIPS_IMAGE_SIZEOF_ELEMENT() to calculate object
  * size.
+ *
+ * It needs to be guint64 and not size_t since we use this as the basis for 
+ * image address calcs and they have to be 64-bit, even on 32-bit machines. 
  */
-const size_t vips__image_sizeof_bandformat[] = {
+const guint64 vips__image_sizeof_bandformat[] = {
 	sizeof( unsigned char ), 	/* VIPS_FORMAT_UCHAR */
 	sizeof( signed char ), 		/* VIPS_FORMAT_CHAR */
 	sizeof( unsigned short ), 	/* VIPS_FORMAT_USHORT */
@@ -202,7 +205,7 @@ const size_t vips__image_sizeof_bandformat[] = {
 
 /* Return number of bytes for a band format, or -1 on error.
  */
-int 
+guint64 
 vips_format_sizeof( VipsBandFormat format )
 {
 	return( (format < 0 || format > VIPS_FORMAT_DPCOMPLEX) ?

libvips/iofuncs/image.c

@@ -566,7 +566,7 @@ vips_image_build( VipsObject *object )
 	const char *mode = image->mode;
 
 	guint32 magic;
-	size_t sizeof_image;
+	guint64 sizeof_image;
 
 	VIPS_DEBUG_MSG( "vips_image_build: %p\n", image );
 
@@ -905,7 +905,7 @@ vips_image_class_init( VipsImageClass *class )
 		G_STRUCT_OFFSET( VipsImage, dhint ),
 		VIPS_TYPE_DEMAND_STYLE, VIPS_DEMAND_STYLE_SMALLTILE );
 
-	VIPS_ARG_INT( class, "sizeof_header", 16, 
+	VIPS_ARG_UINT64( class, "sizeof_header", 16, 
 		_( "Size of header" ), 
 		_( "Offset in bytes from start of file" ),
 		VIPS_ARGUMENT_SET_ONCE | VIPS_ARGUMENT_CONSTRUCT, 
@@ -1395,7 +1395,7 @@ vips_image_new_from_file( const char *filename )
  */
 VipsImage *
 vips_image_new_from_file_raw( const char *filename, 
-	int xsize, int ysize, int bands, int offset )
+	int xsize, int ysize, int bands, guint64 offset )
 {
 	VipsImage *image;
 

libvips/iofuncs/region.c

@@ -934,8 +934,8 @@ vips_region_copy( VipsRegion *reg, VipsRegion *dest, VipsRect *r, int x, int y )
 {
 	int z;
 	int len = VIPS_IMAGE_SIZEOF_PEL( reg->im ) * r->width;
-	char *p = VIPS_REGION_ADDR( reg, r->left, r->top );
+	PEL *p = VIPS_REGION_ADDR( reg, r->left, r->top );
-	char *q = VIPS_REGION_ADDR( dest, x, y );
+	PEL *q = VIPS_REGION_ADDR( dest, x, y );
 	int plsk = VIPS_REGION_LSKIP( reg );
 	int qlsk = VIPS_REGION_LSKIP( dest );
 
@@ -1092,7 +1092,7 @@ vips_region_prepare_to_generate( VipsRegion *reg,
 	VipsRegion *dest, VipsRect *r, int x, int y )
 {
 	IMAGE *im = reg->im;
-	char *p;
+	PEL *p;
 
 	if( !im->generate_fn ) {
 		vips_error( "vips_region_prepare_to",

libvips/iofuncs/window.c

@@ -245,7 +245,7 @@ vips_window_set( VipsWindow *window, int top, int height )
 	window->baseaddr = baseaddr;
 	window->length = pagelength;
 
-	window->data = (char *) baseaddr + (start - pagestart);
+	window->data = (PEL *) baseaddr + (start - pagestart);
 	window->top = top;
 	window->height = height;