572 lines
14 KiB
C
572 lines
14 KiB
C
/* Read a virtual microscope slide using OpenSlide.
|
|
*
|
|
* Benjamin Gilbert
|
|
*
|
|
* Copyright (c) 2011-2015 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
|
|
* 28/2/12
|
|
* - convert "layer" to "level" where externally visible
|
|
* 9/4/12
|
|
* - move argb2rgba back in here, we don't have a use for coded pixels
|
|
* - small cleanups
|
|
* 11/4/12
|
|
* - fail if both level and associated image are specified
|
|
* 20/9/12
|
|
* - update openslide_open error handling for 3.3.0 semantics
|
|
* - switch from deprecated _layer_ functions
|
|
* 11/10/12
|
|
* - look for tile-width and tile-height properties
|
|
* - use threaded tile cache
|
|
* 6/8/13
|
|
* - always output solid (not transparent) pixels
|
|
* 25/1/14
|
|
* - use openslide_detect_vendor() on >= 3.4.0
|
|
* 30/7/14
|
|
* - add autocrop toggle
|
|
* 9/8/14
|
|
* - do argb -> rgba for associated as well
|
|
* 27/1/15
|
|
* - unpremultiplication speedups for fully opaque/transparent pixels
|
|
* 11/7/16
|
|
* - just warn on tile read error
|
|
*/
|
|
|
|
/*
|
|
|
|
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., 51 Franklin Street, Fifth Floor, Boston, MA
|
|
02110-1301 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>
|
|
|
|
#include "openslide2vips.h"
|
|
|
|
typedef struct {
|
|
openslide_t *osr;
|
|
|
|
char *associated;
|
|
|
|
/* Crop to image bounds if @autocrop is set.
|
|
*/
|
|
gboolean autocrop;
|
|
VipsRect bounds;
|
|
|
|
/* Only valid if associated == NULL.
|
|
*/
|
|
int32_t level;
|
|
double downsample;
|
|
uint32_t bg;
|
|
|
|
/* Try to get these from openslide properties.
|
|
*/
|
|
int tile_width;
|
|
int tile_height;
|
|
} ReadSlide;
|
|
|
|
int
|
|
vips__openslide_isslide( const char *filename )
|
|
{
|
|
#ifdef HAVE_OPENSLIDE_3_4
|
|
const char *vendor;
|
|
int ok;
|
|
|
|
vendor = openslide_detect_vendor( filename );
|
|
|
|
/* Generic tiled tiff images can be opened by openslide as well.
|
|
* Only offer to load this file if it's not a generic tiff since
|
|
* we want vips_tiffload() to handle these.
|
|
*/
|
|
ok = ( vendor &&
|
|
strcmp( vendor, "generic-tiff" ) != 0 );
|
|
|
|
VIPS_DEBUG_MSG( "vips__openslide_isslide: %s - %d\n", filename, ok );
|
|
|
|
return( ok );
|
|
#else
|
|
openslide_t *osr;
|
|
int ok;
|
|
|
|
ok = 0;
|
|
osr = openslide_open( filename );
|
|
|
|
if( osr ) {
|
|
const char *vendor;
|
|
|
|
/* Generic tiled tiff images can be opened by openslide as
|
|
* well. Only offer to load this file if it's not a generic
|
|
* tiff since we want vips_tiffload() to handle these.
|
|
*/
|
|
vendor = openslide_get_property_value( osr,
|
|
OPENSLIDE_PROPERTY_NAME_VENDOR );
|
|
|
|
/* vendor will be NULL if osr is in error state.
|
|
*/
|
|
if( vendor &&
|
|
strcmp( vendor, "generic-tiff" ) != 0 )
|
|
ok = 1;
|
|
|
|
openslide_close( osr );
|
|
}
|
|
|
|
VIPS_DEBUG_MSG( "vips__openslide_isslide: %s - %d\n", filename, ok );
|
|
|
|
return( ok );
|
|
#endif
|
|
}
|
|
|
|
static void
|
|
readslide_destroy_cb( VipsImage *image, ReadSlide *rslide )
|
|
{
|
|
VIPS_FREEF( openslide_close, rslide->osr );
|
|
VIPS_FREE( rslide->associated );
|
|
}
|
|
|
|
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( "openslide2vips",
|
|
"%s", _( "invalid associated image name" ) );
|
|
|
|
return( -1 );
|
|
}
|
|
|
|
static gboolean
|
|
get_bounds( openslide_t *osr, VipsRect *rect )
|
|
{
|
|
static const char *openslide_names[] = {
|
|
"openslide.bounds-x",
|
|
"openslide.bounds-y",
|
|
"openslide.bounds-width",
|
|
"openslide.bounds-height"
|
|
};
|
|
static int vips_offsets[] = {
|
|
G_STRUCT_OFFSET( VipsRect, left ),
|
|
G_STRUCT_OFFSET( VipsRect, top ),
|
|
G_STRUCT_OFFSET( VipsRect, width ),
|
|
G_STRUCT_OFFSET( VipsRect, height )
|
|
};
|
|
|
|
const char *value;
|
|
int i;
|
|
|
|
for( i = 0; i < 4; i++ ) {
|
|
if( !(value = openslide_get_property_value( osr,
|
|
openslide_names[i] )) )
|
|
return( FALSE );
|
|
G_STRUCT_MEMBER( int, rect, vips_offsets[i] ) =
|
|
atoi( value );
|
|
}
|
|
|
|
return( TRUE );
|
|
}
|
|
|
|
static ReadSlide *
|
|
readslide_new( const char *filename, VipsImage *out,
|
|
int level, gboolean autocrop, const char *associated )
|
|
{
|
|
ReadSlide *rslide;
|
|
int64_t w, h;
|
|
const char *error;
|
|
const char *background;
|
|
const char * const *properties;
|
|
char *associated_names;
|
|
|
|
if( level &&
|
|
associated ) {
|
|
vips_error( "openslide2vips",
|
|
"%s", _( "specify only one of level or associated "
|
|
"image" ) );
|
|
return( NULL );
|
|
}
|
|
|
|
rslide = VIPS_NEW( out, ReadSlide );
|
|
memset( rslide, 0, sizeof( *rslide ) );
|
|
g_signal_connect( out, "close", G_CALLBACK( readslide_destroy_cb ),
|
|
rslide );
|
|
|
|
rslide->level = level;
|
|
rslide->autocrop = autocrop;
|
|
rslide->associated = g_strdup( associated );
|
|
|
|
/* Non-crazy defaults, override below if we can.
|
|
*/
|
|
rslide->tile_width = 256;
|
|
rslide->tile_height = 256;
|
|
|
|
rslide->osr = openslide_open( filename );
|
|
if( rslide->osr == NULL ) {
|
|
vips_error( "openslide2vips",
|
|
"%s", _( "unsupported slide format" ) );
|
|
return( NULL );
|
|
}
|
|
|
|
error = openslide_get_error( rslide->osr );
|
|
if( error ) {
|
|
vips_error( "openslide2vips",
|
|
_( "opening slide: %s" ), error );
|
|
return( NULL );
|
|
}
|
|
|
|
if( level < 0 ||
|
|
level >= openslide_get_level_count( rslide->osr ) ) {
|
|
vips_error( "openslide2vips",
|
|
"%s", _( "invalid slide level" ) );
|
|
return( NULL );
|
|
}
|
|
|
|
if( associated &&
|
|
check_associated_image( rslide->osr, associated ) )
|
|
return( NULL );
|
|
|
|
if( associated ) {
|
|
openslide_get_associated_image_dimensions( rslide->osr,
|
|
associated, &w, &h );
|
|
vips_image_set_string( out, "slide-associated-image",
|
|
associated );
|
|
vips_image_pipelinev( out, VIPS_DEMAND_STYLE_THINSTRIP, NULL );
|
|
}
|
|
else {
|
|
char buf[256];
|
|
const char *value;
|
|
|
|
openslide_get_level_dimensions( rslide->osr,
|
|
level, &w, &h );
|
|
rslide->downsample = openslide_get_level_downsample(
|
|
rslide->osr, level );
|
|
vips_image_set_int( out, "slide-level", level );
|
|
vips_image_pipelinev( out, VIPS_DEMAND_STYLE_SMALLTILE, NULL );
|
|
|
|
/* Try to get tile width/height. An undocumented, experimental
|
|
* feature.
|
|
*/
|
|
vips_snprintf( buf, 256,
|
|
"openslide.level[%d].tile-width", level );
|
|
if( (value = openslide_get_property_value( rslide->osr, buf )) )
|
|
rslide->tile_width = atoi( value );
|
|
vips_snprintf( buf, 256,
|
|
"openslide.level[%d].tile-height", level );
|
|
if( (value = openslide_get_property_value( rslide->osr, buf )) )
|
|
rslide->tile_height = atoi( value );
|
|
if( value )
|
|
VIPS_DEBUG_MSG( "readslide_new: found tile-size\n" );
|
|
|
|
/* Some images have a bounds in the header. Crop to
|
|
* that if autocrop is set.
|
|
*/
|
|
if( rslide->autocrop )
|
|
if( !get_bounds( rslide->osr, &rslide->bounds ) )
|
|
rslide->autocrop = FALSE;
|
|
if( rslide->autocrop ) {
|
|
VipsRect image;
|
|
|
|
rslide->bounds.left /= rslide->downsample;
|
|
rslide->bounds.top /= rslide->downsample;
|
|
rslide->bounds.width /= rslide->downsample;
|
|
rslide->bounds.height /= rslide->downsample;
|
|
|
|
/* Clip against image size.
|
|
*/
|
|
image.left = 0;
|
|
image.top = 0;
|
|
image.width = w;
|
|
image.height = h;
|
|
vips_rect_intersectrect( &rslide->bounds, &image,
|
|
&rslide->bounds );
|
|
|
|
/* If we've clipped to nothing, ignore bounds.
|
|
*/
|
|
if( vips_rect_isempty( &rslide->bounds ) )
|
|
rslide->autocrop = FALSE;
|
|
}
|
|
if( rslide->autocrop ) {
|
|
w = rslide->bounds.width;
|
|
h = rslide->bounds.height;
|
|
}
|
|
}
|
|
|
|
rslide->bg = 0xffffff;
|
|
if( (background = openslide_get_property_value( rslide->osr,
|
|
OPENSLIDE_PROPERTY_NAME_BACKGROUND_COLOR )) )
|
|
rslide->bg = strtoul( background, NULL, 16 );
|
|
|
|
if( w <= 0 ||
|
|
h <= 0 ||
|
|
rslide->downsample < 0 ) {
|
|
vips_error( "openslide2vips", _( "getting dimensions: %s" ),
|
|
openslide_get_error( rslide->osr ) );
|
|
return( NULL );
|
|
}
|
|
if( w > INT_MAX ||
|
|
h > INT_MAX ) {
|
|
vips_error( "openslide2vips",
|
|
"%s", _( "image dimensions overflow int" ) );
|
|
return( NULL );
|
|
}
|
|
|
|
if( !rslide->autocrop ) {
|
|
rslide->bounds.left = 0;
|
|
rslide->bounds.top = 0;
|
|
rslide->bounds.width = w;
|
|
rslide->bounds.height = h;
|
|
}
|
|
|
|
vips_image_init_fields( out, w, 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_names = g_strjoinv( ", ", (char **)
|
|
openslide_get_associated_image_names( rslide->osr ) );
|
|
vips_image_set_string( out,
|
|
"slide-associated-images", associated_names );
|
|
VIPS_FREE( associated_names );
|
|
|
|
return( rslide );
|
|
}
|
|
|
|
int
|
|
vips__openslide_read_header( const char *filename, VipsImage *out,
|
|
int level, gboolean autocrop, char *associated )
|
|
{
|
|
if( !readslide_new( filename, out, level, autocrop, associated ) )
|
|
return( -1 );
|
|
|
|
return( 0 );
|
|
}
|
|
|
|
/* Convert from ARGB to RGBA and undo premultiplication.
|
|
*
|
|
* We throw away transparency. Formats like Mirax use transparent + bg
|
|
* colour for areas with no useful pixels. But if we output
|
|
* transparent pixels and then convert to RGB for jpeg write later, we
|
|
* would have to pass the bg colour down the pipe somehow. The
|
|
* structure of dzsave makes this tricky.
|
|
*
|
|
* We could output plain RGB instead, but that would break
|
|
* compatibility with older vipses.
|
|
*/
|
|
static void
|
|
argb2rgba( uint32_t * restrict buf, int n, uint32_t bg )
|
|
{
|
|
int i;
|
|
|
|
for( i = 0; i < n; i++ ) {
|
|
uint32_t * restrict p = buf + i;
|
|
uint32_t x = *p;
|
|
uint8_t a = x >> 24;
|
|
VipsPel * restrict out = (VipsPel *) p;
|
|
|
|
if( a == 255 )
|
|
*p = GUINT32_TO_BE( (x << 8) | 255 );
|
|
else if( a == 0 )
|
|
/* Use background color.
|
|
*/
|
|
*p = GUINT32_TO_BE( (bg << 8) | 255 );
|
|
else {
|
|
/* Undo premultiplication.
|
|
*/
|
|
out[0] = 255 * ((x >> 16) & 255) / a;
|
|
out[1] = 255 * ((x >> 8) & 255) / a;
|
|
out[2] = 255 * (x & 255) / a;
|
|
out[3] = 255;
|
|
}
|
|
}
|
|
}
|
|
|
|
static int
|
|
vips__openslide_generate( VipsRegion *out,
|
|
void *_seq, void *_rslide, void *unused, gboolean *stop )
|
|
{
|
|
ReadSlide *rslide = _rslide;
|
|
uint32_t bg = rslide->bg;
|
|
VipsRect *r = &out->valid;
|
|
int n = r->width * r->height;
|
|
uint32_t *buf = (uint32_t *) VIPS_REGION_ADDR( out, r->left, r->top );
|
|
|
|
const char *error;
|
|
|
|
VIPS_DEBUG_MSG( "vips__openslide_generate: %dx%d @ %dx%d\n",
|
|
r->width, r->height, r->left, r->top );
|
|
|
|
/* We're inside a cache, so requests should always be
|
|
* tile_width by tile_height pixels and on a tile boundary.
|
|
*/
|
|
g_assert( (r->left % rslide->tile_width) == 0 );
|
|
g_assert( (r->top % rslide->tile_height) == 0 );
|
|
g_assert( r->width <= rslide->tile_width );
|
|
g_assert( r->height <= rslide->tile_height );
|
|
|
|
/* The memory on the region should be contiguous for our ARGB->RGBA
|
|
* loop below.
|
|
*/
|
|
g_assert( VIPS_REGION_LSKIP( out ) == r->width * 4 );
|
|
|
|
openslide_read_region( rslide->osr,
|
|
buf,
|
|
(r->left + rslide->bounds.left) * rslide->downsample,
|
|
(r->top + rslide->bounds.top) * rslide->downsample,
|
|
rslide->level,
|
|
r->width, r->height );
|
|
|
|
/* Only warn on error: we don't want to make the whole image unreadable
|
|
* because of one broken tile.
|
|
*
|
|
* FIXME ... add a --fail option like jpegload
|
|
*/
|
|
error = openslide_get_error( rslide->osr );
|
|
if( error )
|
|
vips_warn( "openslide2vips",
|
|
_( "reading region: %s" ), error );
|
|
|
|
/* Since we are inside a cache, we know buf must be continuous.
|
|
*/
|
|
argb2rgba( buf, n, bg );
|
|
|
|
return( 0 );
|
|
}
|
|
|
|
int
|
|
vips__openslide_read( const char *filename, VipsImage *out,
|
|
int level, gboolean autocrop )
|
|
{
|
|
ReadSlide *rslide;
|
|
VipsImage *raw;
|
|
VipsImage *t;
|
|
|
|
VIPS_DEBUG_MSG( "vips__openslide_read: %s %d\n",
|
|
filename, level );
|
|
|
|
raw = vips_image_new();
|
|
vips_object_local( out, raw );
|
|
|
|
if( !(rslide = readslide_new( filename, raw,
|
|
level, autocrop, NULL )) )
|
|
return( -1 );
|
|
|
|
if( vips_image_generate( raw,
|
|
NULL, vips__openslide_generate, NULL, rslide, NULL ) )
|
|
return( -1 );
|
|
|
|
/* Copy to out, adding a cache. Enough tiles for a complete row, plus
|
|
* 50%.
|
|
*/
|
|
if( vips_tilecache( raw, &t,
|
|
"tile_width", rslide->tile_width,
|
|
"tile_height", rslide->tile_height,
|
|
"max_tiles",
|
|
(int) (1.5 * (1 + raw->Xsize / rslide->tile_width)),
|
|
"threaded", TRUE,
|
|
NULL ) )
|
|
return( -1 );
|
|
if( vips_image_write( t, out ) ) {
|
|
g_object_unref( t );
|
|
return( -1 );
|
|
}
|
|
g_object_unref( t );
|
|
|
|
return( 0 );
|
|
}
|
|
|
|
int
|
|
vips__openslide_read_associated( const char *filename, VipsImage *out,
|
|
const char *associated )
|
|
{
|
|
ReadSlide *rslide;
|
|
VipsImage *raw;
|
|
uint32_t *buf;
|
|
const char *error;
|
|
|
|
VIPS_DEBUG_MSG( "vips__openslide_read_associated: %s %s\n",
|
|
filename, associated );
|
|
|
|
/* Memory buffer. Get associated directly to this, then copy to out.
|
|
*/
|
|
raw = vips_image_new_memory();
|
|
vips_object_local( out, raw );
|
|
|
|
if( !(rslide = readslide_new( filename, raw, 0, FALSE, associated )) ||
|
|
vips_image_write_prepare( raw ) )
|
|
return( -1 );
|
|
buf = (uint32_t *) VIPS_IMAGE_ADDR( raw, 0, 0 );
|
|
openslide_read_associated_image( rslide->osr, rslide->associated, buf );
|
|
error = openslide_get_error( rslide->osr );
|
|
if( error ) {
|
|
vips_error( "openslide2vips",
|
|
_( "reading associated image: %s" ), error );
|
|
return( -1 );
|
|
}
|
|
argb2rgba( buf, raw->Xsize * raw->Ysize, rslide->bg );
|
|
|
|
if( vips_image_write( raw, out ) )
|
|
return( -1 );
|
|
|
|
return( 0 );
|
|
}
|
|
|
|
#endif /*HAVE_OPENSLIDE*/
|