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

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also, start adding openslide.c to foreign

Conflicts:
	ChangeLog
	TODO
	libvips/iofuncs/image.c
This commit is contained in:
John Cupitt 2011-12-11 15:54:08 +00:00
commit 7fe4843250
27 changed files with 1122 additions and 40 deletions
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1
ChangeLog
View File

@ -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

4
README
View File

@ -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

26
TODO
View File

@ -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?

19
configure.in
View File

@ -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

4
libvips/arithmetic/measure.c
View File

@ -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 );

2
libvips/arithmetic/stats.c
View File

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

1
libvips/colour/Makefile.am
View File

@ -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 \

20
libvips/colour/colour_dispatch.c
View File

@ -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,

110
libvips/colour/im_argb2rgba.c Normal file
View File

@ -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 );
}

2
libvips/conversion/flip.c
View File

@ -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;

8
libvips/conversion/im_subsample.c
View File

@ -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 );
char *p;
PEL *q = IM_REGION_ADDR( or, le, y );
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 );
char *p;
PEL *q = IM_REGION_ADDR( or, le, y );
PEL *p;
/* Loop across the region, in owidth sized pieces.
*/

377
libvips/foreign/openslide.c Normal file
View File

@ -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 );
}

47
libvips/foreign/openslide.h Normal file
View File

@ -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*/

3
libvips/format/Makefile.am
View File

@ -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@

6
libvips/format/format.c
View File

@ -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();

469
libvips/format/openslide.c Normal file
View File

@ -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*/

2
libvips/histograms_lut/im_histnD.c
View File

@ -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:

1
libvips/include/vips/colour.h
View File

@ -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 );

2
libvips/include/vips/header.h
View File

@ -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 );

14
libvips/include/vips/image.h
View File

@ -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 );

13
libvips/include/vips/object.h
View File

@ -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; \

6
libvips/include/vips/private.h
View File

@ -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;

4
libvips/include/vips/region.h
View File

@ -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 ) \

7
libvips/iofuncs/header.c
View File

@ -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) ?

6
libvips/iofuncs/image.c
View File

@ -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;

6
libvips/iofuncs/region.c
View File

@ -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 );
char *q = VIPS_REGION_ADDR( dest, x, y );
PEL *p = VIPS_REGION_ADDR( reg, r->left, r->top );
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",

2
libvips/iofuncs/window.c
View File

@ -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;