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final openslide cleanups

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This commit is contained in:
John Cupitt 2011-12-12 11:58:36 +00:00
parent 05fbb6b3bc
commit 18d54ea3d2
10 changed files with 57 additions and 508 deletions
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46
TODO
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@ -1,27 +1,6 @@
- still some size_t that should be guint64, search for all use of
VIPS_IMAGE_SIZEOF_IMAGE(), vips__parse_size()
- how about
vips max add[babe.jpg,babe2.jpg]
does that make any sense?
vips copy add[babe.jpg,add[babe2.jpg,babe3.jpg]] sum.v
- 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
@ -47,11 +26,6 @@
- see vips_image_cache(): it currently writes to @out allocated by its caller
should this be called vips_image_write_cache()? or wrapped in the style
of vips_copy()?
@ -68,6 +42,26 @@
- how about
vips max add[babe.jpg,babe2.jpg]
does that make any sense?
vips copy add[babe.jpg,add[babe2.jpg,babe3.jpg]] sum.v
- see vips_image_cache(): it currently writes to @out allocated by its caller
should this be called vips_image_write_cache()? or wrapped in the style
of vips_copy()?
- make an argb coding type, add to nip2 and known coding
- nip2 should use zooming support, if possible
- transform_g_string_array_image() can't handle quoted strings, so filenames
with spaces will break

4
libvips/colour/im_argb2rgba.c
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@ -84,7 +84,7 @@ argb2rgba( guint32 *in, PEL *out, int n, void *_bg )
* Returns: 0 on success, -1 on error.
*/
int
im_argb2rgba( IMAGE *in, IMAGE *out )
im_argb2rgba( VipsImage *in, IMAGE *out )
{
guint32 bg;
@ -99,7 +99,7 @@ im_argb2rgba( IMAGE *in, IMAGE *out )
return( -1 );
out->Coding = IM_CODING_NONE;
if( im_meta_get_int( in, "background-rgb", (int *) &bg ) )
if( vips_image_get_int( in, VIPS_META_BACKGROUND_RGB, (int *) &bg ) )
bg = 0xffffff;
if( im_wrapone( in, out,

3
libvips/foreign/foreign.c
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@ -59,7 +59,8 @@
* transparently supported by vips_image_new_from_foreign() and friends.
*
* VIPS comes with VipsForeign for TIFF, JPEG, PNG, Analyze, PPM, OpenEXR, CSV,
* Matlab, Radiance, RAW, VIPS and one that wraps libMagick.
* Matlab, Radiance, RAW and VIPS. It also includes import filters which can
* load with libMagick and with OpenSlide.
*/
/**

5
libvips/foreign/openslide2vips.c
View File

@ -189,9 +189,10 @@ readslide_new( const char *filename, VipsImage *out,
OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR );
if( background != NULL )
vips_image_set_int( out,
"background-rgb", strtoul( background, NULL, 16 ) );
VIPS_META_BACKGROUND_RGB,
strtoul( background, NULL, 16 ) );
else
vips_image_set_int( out, "background-rgb", 0xffffff );
vips_image_set_int( out, VIPS_META_BACKGROUND_RGB, 0xffffff );
if( w < 0 || h < 0 || rslide->downsample < 0 ) {
vips_error( "openslide2vips", _( "getting dimensions: %s" ),

18
libvips/foreign/openslideload.c
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@ -116,6 +116,13 @@ vips_foreign_load_openslide_load( VipsForeignLoad *load )
return( 0 );
}
static void
vips_foreign_load_openslide_error_handler( const char *domain,
GLogLevelFlags level, const char *message, void *data )
{
vips_error( "openslide", "%s", message );
}
static void
vips_foreign_load_openslide_class_init( VipsForeignLoadOpenslideClass *class )
{
@ -161,6 +168,12 @@ vips_foreign_load_openslide_class_init( VipsForeignLoadOpenslideClass *class )
VIPS_ARGUMENT_OPTIONAL_INPUT,
G_STRUCT_OFFSET( VipsForeignLoadOpenslide, associated ),
NULL );
/* Catch just openslide errors.
*/
g_log_set_handler( "Openslide",
G_LOG_LEVEL_CRITICAL | G_LOG_LEVEL_WARNING,
vips_foreign_load_openslide_error_handler, NULL );
}
static void
@ -189,10 +202,13 @@ vips_foreign_load_openslide_init( VipsForeignLoadOpenslide *openslide )
* 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,
* set @associated to the image's.
* set @associated to the image's name.
* A slide's associated images are listed in the
* "slide-associated-images" metadata item.
*
* The output of this operator is in pre-multipled ARGB format. Use
* im_argb2rgba() to decode to png-style RGBA.
*
* See also: vips_image_new_from_file().
*
* Returns: 0 on success, -1 on error.

3
libvips/format/Makefile.am
View File

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

4
libvips/format/format.c
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@ -464,10 +464,6 @@ 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
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@ -1,469 +0,0 @@
/* 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*/

8
libvips/include/vips/header.h
View File

@ -77,6 +77,14 @@ extern "C" {
*/
#define VIPS_META_RESOLUTION_UNIT "resolution-unit"
/**
* VIPS_META_BACKGROUND_RGB:
*
* The OpenSlide load operator uses this to note the colour to use to paint
* transparent pixels in pre-multiplied ARGB format. See im_argb2rgba().
*/
#define VIPS_META_BACKGROUND_RGB "background-rgb"
guint64 vips_format_sizeof( VipsBandFormat format );
int vips_image_get_width( const VipsImage *image );

5
libvips/include/vips/image.h
View File

@ -411,7 +411,10 @@ typedef struct _VipsImageClass {
GType vips_image_get_type( void );
extern const size_t vips__image_sizeof_bandformat[];
/* Has to be guint64 and not size_t/off_t since we have to be able to address
* huge images on platforms with 32-bit files.
*/
extern const guint64 vips__image_sizeof_bandformat[];
/* Pixel address calculation macros.
*/